In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

baseDir <- "/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette"
library(stringr)
library(CLIPflexR)
library(SummarizedExperiment)
library(GenomicRanges)
library(rtracklayer)

Process standard/BrdU-CLIP libraries using CLIPflexR

This is an alternative to the CTK processing pipeline for CLIP data, and returns a peak matrix with genomic locations of peaks and counts in each peak by sample

Initial processing and quality control

Decompress fastq files

Use compressed fastq files as input; R-wrapped decompression function using bzip2.
CLIPflexR documentation

#define the path to your compressed fastq file(s)
#here we have one example fastq.gz generated by standard CLIP (linker ligations; KRG092419_S1_L001_R1_001.fastq.gz)
#and one example fastq.gz generated by BrdU-CLIP (KRG091819_S1_L001_R1_001.fastq.gz)
testFQ <- dir(baseDir, pattern = ".gz", full.names = TRUE)
testFQ

## [1] "/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG091819_S1_L001_R1_001.fastq.gz"
## [2] "/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG092419_S1_L001_R1_001.fastq.gz"

FqFile <- lapply(testFQ, decompress, overwrite=TRUE)
FqFile

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## [1] "/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG091819_S1_L001_R1_001.fastq"
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## [1] "/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG092419_S1_L001_R1_001.fastq"

You can look at the quality of your data (wrapping FASTX's quality stats)

Get quality statistics from your run using R-wrapped fastx_quality_stats from FASTX_toolkit.
CLIPflexR documentation

#defaults are set for illumina quality encoding, minimum quality score of 20 for 80% of bases
stats <- lapply(FqFile, fastx_quality_stats)
stats

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## [1] "/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG091819_S1_L001_R1_001.txt"
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## [1] "/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG092419_S1_L001_R1_001.txt"

stats <- read.delim(stats[[1]],header = T, sep = "\t")
head(stats)

##   column    count min max       sum  mean Q1 med Q3 IQR lW rW A_Count
## 1      1 22052373  16  36 712698638 32.32 32  33 34   2 29 36 7104877
## 2      2 22052373   2  36 696285989 31.57 32  33 34   2 29 36 6911254
## 3      3 22052373  16  36 717065818 32.52 32  33 34   2 29 36 7053127
## 4      4 22052373  16  36 718409762 32.58 32  33 34   2 29 36 7049046
## 5      5 22052373  16  36 715824000 32.46 32  33 34   2 29 36 7020505
## 6      6 22052373  14  37 775710593 35.18 34  37 37   3 30 37 6997082
##   C_Count G_Count T_Count N_Count Max_count
## 1 4814492 3873005 6259999       0  22052373
## 2 4622185 3607472 6192199  719263  22052373
## 3 5082531 3618036 6298679       0  22052373
## 4 5060538 3650501 6292288       0  22052373
## 5 5121322 3657985 6252561       0  22052373
## 6 5109816 3666739 6278736       0  22052373

Quality filter (wrapping FastX's quality filter)

Filtering fastq files using R-wrapped fastq_quality_filter from FASTX_toolkit.
qEncoding: Quality encoding, default = 33 (corresponds to Illumina and Sanger quality scores); minimumQuality: minimum quality score to keep, default = 20. Only keep reads with quality score greater than this threshold. minimumPercentOfRead: minimum percent of bases that must have [-q] minimumQuality.
CLIPflexR documentation

FqFile_QF <- lapply(FqFile, fastq_quality_filter)
FqFile_QF

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## [1] "/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/QF_KRG091819_S1_L001_R1_001.fastq"
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## [1] "/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/QF_KRG092419_S1_L001_R1_001.fastq"

Fastx_collapser (wrapping FASTX's fastx_collapser)

Collapse duplicate sequences into unique reads using R-wrapped fastx_collapser from FASTX_toolkit.
qEncoding: Quality encoding, default = 33 (corresponds to Illumina and Sanger quality scores).
CLIPflexR documentation

coll_FqFile_QF <- lapply(FqFile_QF, fastx_collapser)
coll_FqFile_QF

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## [1] "/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/QF_KRG092419_S1_L001_R1_001_collapse.fasta"

Follow these steps to process standard CLIP libraries

De-multiplex samples (wrapping FASTX's barcode splitter)

De-multiplex samples by indices using R-wrapped fastx_barcode_splitter from FASTX_toolkit.
mismatches: number of mismatches allowed in barcode sequence, 0 (default); bcFile: barcode file, see example below.
CLIPflexR documentation

#provide the path to your barcode file,  which must contain one sample name and its corresponding index sequence for  each line, and be tab delimited

#For example:
#Aag2_rIgG_Exp6A CGATG
#Aag2_rIgG_Exp6B TTAGG

BCfile <- dir(baseDir, pattern="BC",  full.names = TRUE)
BCfile <- grep("stats", BCfile, value =T, invert = T)
BCfile

## [1] "/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG091819_BC.txt"
## [2] "/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG092419_BC.txt"

#take standard libraries only
samples_split_std <- fastx_barcode_splitter(coll_FqFile_QF[[2]], bcFile = BCfile[[2]], verbose = TRUE)

## barcode_splitter command is cat /Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/QF_KRG092419_S1_L001_R1_001_collapse.fasta | /Users/kathryn/Library/r-miniconda/envs/CLIPflexR_0.1.19/bin/fastx_barcode_splitter.pl --bcfile /Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG092419_BC.txt --bol --mismatches 0 --prefix '/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG092419_S1_L001_R1_001_collapse_'

## barcode_splitter arguments are  --bcfile /Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG092419_BC.txt--bol--mismatches 0 --prefix '/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG092419_S1_L001_R1_001_collapse_'

#files will be written with a prefix appended for the run, and then the sample name given in the barcode file
#split samples will not have an extension but will be in FASTA format
samples_split_std

##  [1] "/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG092419_S1_L001_R1_001_collapse_Aag2_Ago1_Exp7A"   
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## [14] "/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG092419_S1_L001_R1_001_collapse_aegypti_mIgG_Exp7D"

#sample_stats will also be written, and contain how many reads were extracted for each sample and the file name for that run ID
std_samples_stats <- read.delim(paste0(baseDir, "/KRG092419_BC_stats.txt"), header = T, sep =  "\t")
head(std_samples_stats)

##           Barcode  Count
## 1 Aag2_Ago1_Exp7A 612767
## 2 Aag2_Ago1_Exp7B 579807
## 3 Aag2_Ago2_Exp7A 894236
## 4 Aag2_Ago2_Exp7B 701068
## 5 Aag2_mIgG_Exp7A 310822
## 6 Aag2_mIgG_Exp7B  46491
##                                                                                                                 Location
## 1 /Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG092419_S1_L001_R1_001_collapse_Aag2_Ago1_Exp7A
## 2 /Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG092419_S1_L001_R1_001_collapse_Aag2_Ago1_Exp7B
## 3 /Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG092419_S1_L001_R1_001_collapse_Aag2_Ago2_Exp7A
## 4 /Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG092419_S1_L001_R1_001_collapse_Aag2_Ago2_Exp7B
## 5 /Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG092419_S1_L001_R1_001_collapse_Aag2_mIgG_Exp7A
## 6 /Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG092419_S1_L001_R1_001_collapse_Aag2_mIgG_Exp7B

Now remove the 5' index, linker, and random barcode sequences (wrapping CTK's stripBarcode.pl)

Strip random barcodes/linkers with specific length from reads using R-wrapped stripBarcode.pl from CTK.
linkerlength: barcode length; inputformat: format of input sequences, fasta (default).
CLIPflexR documentation

samples_split_std_rm5 <- lapply(samples_split_std, ctk_stripBarcode, linkerlength = 27, inputFormat="fasta")
samples_split_std_rm5

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Now remove the 3' linker (wrapping FASTX's clipper)

Trimming 3'-end adapter sequences using R-wrapped fastx_clipper function from FASTX_toolkit.
adapter: clip this sequence from the 3'-end of reads, "GTGTCAGTCACTTCCAGCGG" (default); length: minimum read length, only keep reads with length equal or greater then this threshold, 18 (default).
CLIPflexR documentation

samples_split_std_rm5_rm3 <- lapply(samples_split_std_rm5, fastx_clipper, length = 18, adapter="GTGTCAGTCACTTCCAGCGG")
samples_split_std_rm5_rm3

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These reads are now ready to map to your genome

Follow these steps to process BrdU-CLIP libraries

First strip random barcode sequences (UMI) from the 5' end of reads (wrapping CTK's stripBarcode.pl)

BrdU_rm5 <- ctk_stripBarcode(coll_FqFile_QF[[1]], linkerlength = 7, inputFormat="fasta")
BrdU_rm5

## [1] "/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/QF_KRG091819_S1_L001_R1_001_collapse_rm5.fasta"

De-multiplex samples (wrapping FASTX's barcode splitter)

samples_split_BrdU <- fastx_barcode_splitter(BrdU_rm5, bcFile = BCfile[[1]], verbose = TRUE)

## barcode_splitter command is cat /Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/QF_KRG091819_S1_L001_R1_001_collapse_rm5.fasta | /Users/kathryn/Library/r-miniconda/envs/CLIPflexR_0.1.19/bin/fastx_barcode_splitter.pl --bcfile /Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG091819_BC.txt --bol --mismatches 0 --prefix '/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG091819_S1_L001_R1_001_collapse_rm5_'

## barcode_splitter arguments are  --bcfile /Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG091819_BC.txt--bol--mismatches 0 --prefix '/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG091819_S1_L001_R1_001_collapse_rm5_'

#files will be written with a prefix appended for the run, and then the sample name given in the barcode file
#split samples will not have an extension but will be in FASTA format
samples_split_BrdU

##  [1] "/Users/kathryn/Reprocess_all_paper_datasets/test_processing_vignette/KRG091819_S1_L001_R1_001_collapse_rm5_Aag2_Ago1_Exp6A"   
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#sample_stats will also be written, and contain how many reads were extracted for each sample and the file name for that run ID
BrdU_samples_stats <- read.delim(paste0(baseDir, "/KRG091819_BC_stats.txt"), header = T, sep =  "\t")
head(BrdU_samples_stats)

##           Barcode  Count
## 1 Aag2_Ago1_Exp6A 491943
## 2 Aag2_Ago1_Exp6B 507596
## 3 Aag2_Ago2_Exp6A 673944
## 4 Aag2_Ago2_Exp6B 393337
## 5 Aag2_mIgG_Exp6A   1688
## 6 Aag2_mIgG_Exp6B    926
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Trim 3 "not G" (DDD) and index (6nt) from the 5' end of reads (wrapping FASTX's fastx_trimmer)

Trimming 5'-end adapter sequences using R-wrapped fastx_trimmer function from FASTX_toolkit.
read_start: read starts at this base, 10 (default); read_end: read ends at this base, NULL (default).
CLIPflexR documentation

BrdU_split_rm5 <- lapply(samples_split_BrdU, fastx_trimmer, read_start = 10)
BrdU_split_rm5

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Fastx_clipper (wrapping FASTX's fastx_clipper)

BrdU_split_rm5_rm3 <- lapply(BrdU_split_rm5, fastx_clipper, length = 18, adapter="GTGTCAGTCACTTCCAGCGG")
BrdU_split_rm5_rm3

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These reads are now ready to map to your genome

Build a Bowtie2 genome index and align to genome using Rbowtie2.

Build Bowtie2 index of reference genome, AaegL5 in this vignette.
Index documentation; see also CTK processing vignette.

Align reads to genome by bowtie.
format: format of input sequences, fasta (default) or fastq; threads: number of threads used, 1 (default); mode: "genome_map" (default, for mapping reads to a genome) or "reverse_map" (for mapping short sequences such as miRNAs to reads); mode can be set to NULL to set parameters manually
see bowtie_align documentation; see also Rbowtie2

#you will need to get the genome fasta of your organism and input the path to this fasta
genomeFasta <- paste0(baseDir, "/Aedes-aegypti-LVP_AGWG_CHROMOSOMES_AaegL5.fa")

#make index; this step may take a long time and is therefore commented out but shown to illustrate how to execute the function
#building the index only needs to be done the first time you map to a given genome

#genomeIndex <- bowtie2_index(genomeFasta)

#If your genome index is already made, you can simply point to the index
genomeIndex  <- paste0(baseDir, "/Aedes-aegypti-LVP_AGWG_CHROMOSOMES_AaegL5")

#Here I am selecting just a few samples for illustrative purposes. To run all your samples, you would do:
#tomap <- c(BrdU_split_rm5_rm3, samples_split_std_rm5_rm3)
tomap <- c(BrdU_split_rm5_rm3[1:2], samples_split_std_rm5_rm3[1:2])  # all I am doing here is taking samples 1-4 for each set of processed files (BrdU and standard) for mapping
tomap

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#map files to genome with default parameters: maxMismatches=1,seedSubString=18,threads=1,report_k=NULL
bams <- lapply(tomap, bowtie_align, genomeIndex, mode = "genome_map")
bams

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Convert to beds, find peaks, and build count matrix

Convert to beds

CLIPflexR documentation

beds <- lapply(bams, bamtobed)
beds

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Make tag directories and findpeaks (wrapping HOMER's MakeTagDirectory and findpeaks)

Call significant peaks in each sample using R-wrapped homer_peaks from HOMER makeTagDirectory & HOMER findpeaks.
style: type of HOMER peak calling, "factor" (default); foldEnrichmentOverLocal: fold enrichment over local tag count, 2 (default); localSize:region to check for local tag enrichment, 10000 (default); strand: find peaks using tags on "seperate" (default); minDist: minimum distance between peaks, 50 (default); size: peak size, 10 (default); fragLength: approximate fragment length, 10 (default); genomeSize: NULL=2e9 (default, human or mouse), or set for your genome.
CLIPflexR documentation

#you may want to play with these parameters depending on your protein of interest, and ensure that coverage lines up with the peaks you have called
peaks <- lapply(beds, homer_peaks, fragLength=25)

Make count matrix of peaks, starting with reading in HOMER peak files and making a matrix that indicated which peaks were called in each sample

#read in peak files and convert to GRanges
read_peaks <- lapply(peaks,function(x)read.delim(x,sep="\t",comment.char = "#",h=FALSE))
read_peaksGR <- lapply(read_peaks,
                       function(x)GRanges(x$V2,IRanges(x$V3,x$V4),strand = x$V5))
names(read_peaksGR) <- gsub( paste0(baseDir,"/"), "",  (unlist(peaks)))
read_peaksGRList <- GRangesList(read_peaksGR)
GRSet <- unlist(read_peaksGRList)
nGRSet <- reduce(GRSet)
peakmat <- do.call(cbind,lapply(read_peaksGRList,
                                function(x)
                                  nGRSet %over% x))
mcols(nGRSet) <- peakmat

#now you have a peakmat where rows are a reduced set of peaks (without an identifier for the time being), and each column  is whether or not the peak was called in that sample
head(peakmat)

##      KRG091819_S1_L001_R1_001_collapse_rm5_Aag2_Ago1_Exp6A_trim_clip/peaks.txt
## [1,]                                                                     FALSE
## [2,]                                                                     FALSE
## [3,]                                                                     FALSE
## [4,]                                                                      TRUE
## [5,]                                                                     FALSE
## [6,]                                                                      TRUE
##      KRG091819_S1_L001_R1_001_collapse_rm5_Aag2_Ago1_Exp6B_trim_clip/peaks.txt
## [1,]                                                                     FALSE
## [2,]                                                                     FALSE
## [3,]                                                                     FALSE
## [4,]                                                                     FALSE
## [5,]                                                                      TRUE
## [6,]                                                                     FALSE
##      KRG092419_S1_L001_R1_001_collapse_Aag2_Ago1_Exp7A_rm5_clip/peaks.txt
## [1,]                                                                FALSE
## [2,]                                                                 TRUE
## [3,]                                                                 TRUE
## [4,]                                                                FALSE
## [5,]                                                                FALSE
## [6,]                                                                FALSE
##      KRG092419_S1_L001_R1_001_collapse_Aag2_Ago1_Exp7B_rm5_clip/peaks.txt
## [1,]                                                                 TRUE
## [2,]                                                                FALSE
## [3,]                                                                FALSE
## [4,]                                                                FALSE
## [5,]                                                                 TRUE
## [6,]                                                                FALSE

The next step is to countFromBed to append the number of reads at each peak location, by sample

CLIPflexR documentation

#defaults are: notStranded=TRUE,interFeature=FALSE
countmat <- lapply(beds,countFromBed,GR=nGRSet)

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': NIGP01000917, NIGP01002025
##   - in 'y': NIGP01002089, NIGP01000727, NIGP01000475, NIGP01002221, NIGP01001492, NIGP01000892, NIGP01000201, NIGP01001727, NIGP01001982, NIGP01000101, NIGP01002078, NIGP01001086, NIGP01002082, NIGP01002045, NIGP01002203, NIGP01000451, NIGP01000495, NIGP01002020, NIGP01001844, NIGP01002286, NIGP01002127, NIGP01000184, NIGP01000944, NIGP01000304, NIGP01000130, NIGP01001935, NIGP01000647, NIGP01002035, NIGP01001914, NIGP01001774, NIGP01000058, NIGP01000662, NIGP01000976, NIGP01000253, NIGP01001770, NIGP01000416, NIGP01001671, NIGP01001712, NIGP01002113, NIGP01001514, NIGP01000379, NIGP01000036, NIGP01002034, NIGP01000552, NIGP01000094, NIGP01001837, NIGP01001551, NIGP01000525, NIGP01002215, NIGP01001678, NIGP01000638, NIGP01001599, NIGP01000106, NIGP01001294, NIGP01002178, NIGP01000256, NIGP01000283, NIGP01001031, NIGP01002155, NIGP01000077, NIGP01001793, NIGP01000371, NIGP01000658, NIGP01001480, NIGP01000848, NIGP01000415, NIGP01000180, NIGP01001039, NIGP01000110, NIGP01000242, NIGP01001503, NIGP01001976, NIGP01000537, NIGP01000565, NIGP01000807, NIGP01002168, NIGP01000482, NIGP01002289, NIGP01000751, NIGP01001945, NIGP01000574, NIGP01002209, NIGP01001759, NIGP01000402, NIGP01000198, NIGP01000292, NIGP01002029, NIGP01000294, NIGP01000909, NIGP01000139, NIGP01000282, NIGP01001786, NIGP01000376, NIGP01001698, NIGP01001206, NIGP01002240, NIGP01001030, NIGP01001414, NIGP01001750, NIGP01002188, NIGP01000072, NIGP01000080, NIGP01002269, NIGP01000033, NIGP01001661, NIGP01002234, NIGP01000761, NIGP01000063, NIGP01002251, NIGP01002176, NIGP01000433, NIGP01000034, NIGP01000159, NIGP01000575, NIGP01002300, NIGP01001458, NIGP01001507, NIGP01000182, NIGP01000941, NIGP01000188, NIGP01002297, NIGP01000697, NIGP01000629, NIGP01001062, NIGP01001508, NIGP01002230, NIGP01000197, NIGP01000266, NIGP01000699, NIGP01000541, NIGP01001755, NIGP01001696, NIGP01000656, NIGP01000563, NIGP01000888, NIGP01000327, NIGP01001988, NIGP01001641, NIGP01001846, NIGP01001908, NIGP01000986, NIGP01001769, NIGP01000440, NIGP01002046, NIGP01000505, NIGP01002152, NIGP01000627, NIGP01000598, NIGP01000274, NIGP01000414, NIGP01002253, NIGP01001029, NIGP01000599, NIGP01001510, NIGP01001887, NIGP01001615, NIGP01000650, NIGP01000735, NIGP01002199, NIGP01001036, NIGP01002153, NIGP01001949, NIGP01002196, NIGP01000407, NIGP01000437, NIGP01001919, NIGP01000809, NIGP01001929, NIGP01001703, NIGP01001866, NIGP01000504, NIGP01001327, NIGP01002058, NIGP01000779, NIGP01001557, NIGP01002024, NIGP01000859, NIGP01000206, NIGP01000189, NIGP01000210, NIGP01001019, NIGP01001717, NIGP01002087, NIGP01001650, NIGP01001845, NIGP01000361, NIGP01000579, NIGP01001741, NIGP01000205, NIGP01000802, NIGP01000548, NIGP01001757, NIGP01000356, NIGP01000893, NIGP01000637, NIGP01001469, NIGP01000780, NIGP01001915, NIGP01001943, NIGP01000335, NIGP01001933, NIGP01000920, NIGP01000863, NIGP01000417, NIGP01000845, NIGP01001008, NIGP01001803, NIGP01000039, NIGP01001816, NIGP01000665, NIGP01000818, NIGP01000521, NIGP01000578, NIGP01000532, NIGP01000821, NIGP01001546, NIGP01002242, NIGP01000384, NIGP01000295, NIGP01000408, NIGP01001940, NIGP01001566, NIGP01000865, NIGP01000646, NIGP01000187, NIGP01000962, NIGP01001024, NIGP01001076, NIGP01000497, NIGP01000916, NIGP01001927, NIGP01000791, NIGP01000760, NIGP01001028, NIGP01000124, NIGP01002055, NIGP01000212, NIGP01001898, NIGP01000149, NIGP01002044, NIGP01000363, NIGP01000904, NIGP01002133, NIGP01000123, NIGP01001567, NIGP01001956, NIGP01000232, NIGP01002275, NIGP01000142, NIGP01000413, NIGP01001736, NIGP01000728, NIGP01000608, NIGP01000290, NIGP01000477, NIGP01000806, NIGP01000315, NIGP01001858, NIGP01000577, NIGP01001066, NIGP01001934, NIGP01001767, NIGP01000573, NIGP01000648, NIGP01000747, NIGP01000397, NIGP01002103, NIGP01000600, NIGP01002121, NIGP01000254, NIGP01001977, NIGP01000959, NIGP01000009, NIGP01000640, NIGP01000061, NIGP01002278, NIGP01001893, NIGP01001584, NIGP01000218, NIGP01000148, NIGP01000711, NIGP01001875, NIGP01001085, NIGP01000463, NIGP01001536, NIGP01001672, NIGP01000450, NIGP01000736, NIGP01000281, NIGP01000031, NIGP01001758, NIGP01000840, NIGP01001961, NIGP01001925, NIGP01001554, NIGP01001764, NIGP01000098, NIGP01000457, NIGP01001690, NIGP01001534, NIGP01001942, NIGP01000216, NIGP01000965, NIGP01000328, NIGP01001909, NIGP01001392, NIGP01000522, NIGP01000213, NIGP01001593, NIGP01000464, NIGP01000456, NIGP01001540, NIGP01002260, NIGP01000279, NIGP01001061, NIGP01002191, NIGP01002064, NIGP01000486, NIGP01000775, NIGP01001847, NIGP01001688, NIGP01000963, NIGP01002181, NIGP01002014, NIGP01000424, NIGP01002179, NIGP01001077, NIGP01000870, NIGP01000580, NIGP01000056, NIGP01001498, NIGP01000639, NIGP01000768, NIGP01000745, NIGP01001781, NIGP01000813, NIGP01000666, NIGP01002099, NIGP01000092, NIGP01000885, NIGP01000700, NIGP01001634, NIGP01000381, NIGP01000645, NIGP01000958, NIGP01000620, NIGP01000263, NIGP01000896, NIGP01000046, NIGP01000025, NIGP01000378, NIGP01000403, NIGP01001639, NIGP01000185, NIGP01001561, NIGP01001601, NIGP01002009, NIGP01000095, NIGP01001704, NIGP01001053, NIGP01000194, NIGP01000866, NIGP01001497, NIGP01000568, NIGP01001017, NIGP01002126, NIGP01000369, NIGP01000020, NIGP01001573, NIGP01000291, NIGP01002170, NIGP01001430, NIGP01002096, NIGP01002167, NIGP01000257, NIGP01000996, NIGP01000670, NIGP01001810, NIGP01000476, NIGP01001928, NIGP01001082, NIGP01000950, NIGP01000759, NIGP01001635, NIGP01000737, NIGP01001415, NIGP01000060, NIGP01002207, NIGP01002077, NIGP01000680, NIGP01000052, NIGP01000121, NIGP01000113, NIGP01000144, NIGP01002154, NIGP01000975, NIGP01002157, NIGP01000269, NIGP01001072, NIGP01000088, NIGP01000583, NIGP01000426, NIGP01002163, NIGP01000581, NIGP01000125, NIGP01000247, NIGP01001791, NIGP01001499, NIGP01001676, NIGP01001711, NIGP01001902, NIGP01000480, NIGP01001035, NIGP01000709, NIGP01001763, NIGP01000367, NIGP01000597, NIGP01001068, NIGP01002146, NIGP01000473, NIGP01001748, NIGP01001728, NIGP01000823, NIGP01000103, NIGP01002106, NIGP01000014, NIGP01000134, NIGP01002065, NIGP01001707, NIGP01000203, NIGP01000657, NIGP01002263, NIGP01001737, NIGP01002169, NIGP01001819, NIGP01000280, NIGP01002151, NIGP01001833, NIGP01001708, NIGP01002273, NIGP01001084, NIGP01001059, NIGP01000596, NIGP01001807, NIGP01000375, NIGP01000507, NIGP01000714, NIGP01001673, NIGP01001880, NIGP01000852, NIGP01002042, NIGP01000489, NIGP01000757, NIGP01000340, NIGP01000447, NIGP01001805, NIGP01000374, NIGP01001700, NIGP01000713, NIGP01000069, NIGP01002122, NIGP01000734, NIGP01000047, NIGP01001958, NIGP01001890, NIGP01000453, NIGP01001994, NIGP01000805, NIGP01001749, NIGP01001979, NIGP01000621, NIGP01000694, NIGP01000972, NIGP01001968, NIGP01001839, NIGP01001989, NIGP01001960, NIGP01000209, NIGP01002187, NIGP01002001, NIGP01001813, NIGP01000150, NIGP01000991, NIGP01002084, NIGP01000514, NIGP01002039, NIGP01001739, NIGP01000157, NIGP01001842, NIGP01001073, NIGP01000005, NIGP01000285, NIGP01001281, NIGP01001572, NIGP01000786, NIGP01001867, NIGP01002158, NIGP01001521, NIGP01000084, NIGP01001517, NIGP01002189, NIGP01000919, NIGP01001530, NIGP01000635, NIGP01000107, NIGP01000204, NIGP01000644, NIGP01001014, NIGP01002228, NIGP01000228, NIGP01002264, NIGP01000557, NIGP01000329, NIGP01001630, NIGP01002110, NIGP01000246, NIGP01000049, NIGP01002128, NIGP01001439, NIGP01002101, NIGP01001952, NIGP01000999, NIGP01000411, NIGP01001146, NIGP01001074, NIGP01000750, NIGP01000096, NIGP01001811, NIGP01002308, NIGP01000718, NIGP01002193, NIGP01000938, NIGP01000053, NIGP01001041, NIGP01001595, NIGP01001752, NIGP01001733, NIGP01000547, NIGP01000710, NIGP01002177, NIGP01001230, NIGP01001533, NIGP01001691, NIGP01001301, NIGP01000667, NIGP01000617, NIGP01000441, NIGP01001240, NIGP01001991, NIGP01001046, NIGP01000041, NIGP01002130, NIGP01000633, NIGP01000907, NIGP01001018, NIGP01000832, NIGP01001519, NIGP01001153, NIGP01000017, NIGP01001217, NIGP01000654, NIGP01001795, NIGP01000422, NIGP01000967, NIGP01000942, NIGP01000609, NIGP01000560, NIGP01000401, NIGP01001081, NIGP01000652, NIGP01001783, NIGP01000177, NIGP01000882, NIGP01001067, NIGP01000326, NIGP01002229, NIGP01

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': NIGP01001735
##   - in 'y': NIGP01002089, NIGP01000727, NIGP01000475, NIGP01002221, NIGP01001492, NIGP01000892, NIGP01000201, NIGP01001727, NIGP01001982, NIGP01000101, NIGP01002078, NIGP01001086, NIGP01002082, NIGP01002045, NIGP01002203, NIGP01000451, NIGP01000495, NIGP01002020, NIGP01001844, NIGP01002286, NIGP01002127, NIGP01000184, NIGP01000944, NIGP01000304, NIGP01000130, NIGP01001935, NIGP01000647, NIGP01002035, NIGP01001914, NIGP01001774, NIGP01000058, NIGP01000662, NIGP01000976, NIGP01000253, NIGP01001770, NIGP01000416, NIGP01001671, NIGP01001712, NIGP01002113, NIGP01001514, NIGP01000379, NIGP01000036, NIGP01002034, NIGP01000552, NIGP01000094, NIGP01001837, NIGP01001551, NIGP01000525, NIGP01002215, NIGP01001678, NIGP01000638, NIGP01001599, NIGP01000106, NIGP01001294, NIGP01002178, NIGP01000256, NIGP01000283, NIGP01001031, NIGP01002155, NIGP01000077, NIGP01001793, NIGP01000371, NIGP01000658, NIGP01001480, NIGP01000848, NIGP01000415, NIGP01001039, NIGP01000110, NIGP01000242, NIGP01001503, NIGP01001976, NIGP01000537, NIGP01000565, NIGP01000807, NIGP01002168, NIGP01000593, NIGP01000482, NIGP01002289, NIGP01000751, NIGP01001945, NIGP01000574, NIGP01002209, NIGP01001759, NIGP01000402, NIGP01000198, NIGP01000432, NIGP01000292, NIGP01002029, NIGP01000294, NIGP01000909, NIGP01000139, NIGP01000282, NIGP01001786, NIGP01000376, NIGP01001698, NIGP01001206, NIGP01002240, NIGP01001030, NIGP01001414, NIGP01001750, NIGP01002188, NIGP01000072, NIGP01000080, NIGP01002269, NIGP01000033, NIGP01001661, NIGP01002234, NIGP01000602, NIGP01000761, NIGP01000063, NIGP01002251, NIGP01002176, NIGP01000433, NIGP01000034, NIGP01000159, NIGP01000575, NIGP01002300, NIGP01001458, NIGP01001507, NIGP01000941, NIGP01000188, NIGP01002297, NIGP01000629, NIGP01001062, NIGP01001508, NIGP01002230, NIGP01000197, NIGP01000699, NIGP01000541, NIGP01001755, NIGP01000656, NIGP01000563, NIGP01000888, NIGP01000327, NIGP01001988, NIGP01001641, NIGP01001846, NIGP01001908, NIGP01000986, NIGP01001769, NIGP01000440, NIGP01002046, NIGP01002152, NIGP01000627, NIGP01000274, NIGP01000414, NIGP01002253, NIGP01001029, NIGP01000599, NIGP01001510, NIGP01001887, NIGP01001615, NIGP01000650, NIGP01000735, NIGP01002199, NIGP01001036, NIGP01002153, NIGP01001949, NIGP01002196, NIGP01000407, NIGP01000437, NIGP01001919, NIGP01000809, NIGP01001929, NIGP01001703, NIGP01001866, NIGP01000504, NIGP01001327, NIGP01002058, NIGP01000779, NIGP01001557, NIGP01000859, NIGP01000206, NIGP01000189, NIGP01000210, NIGP01001019, NIGP01001717, NIGP01002087, NIGP01001650, NIGP01001845, NIGP01000361, NIGP01000579, NIGP01001741, NIGP01000205, NIGP01000802, NIGP01000548, NIGP01000356, NIGP01000893, NIGP01001469, NIGP01000780, NIGP01001915, NIGP01001943, NIGP01000335, NIGP01001933, NIGP01000920, NIGP01000863, NIGP01000417, NIGP01000845, NIGP01001008, NIGP01001803, NIGP01000039, NIGP01001816, NIGP01000665, NIGP01000818, NIGP01000521, NIGP01000578, NIGP01000532, NIGP01000821, NIGP01001546, NIGP01002242, NIGP01000384, NIGP01000295, NIGP01000471, NIGP01000408, NIGP01001940, NIGP01001566, NIGP01000865, NIGP01000646, NIGP01000187, NIGP01000316, NIGP01001024, NIGP01001076, NIGP01000497, NIGP01000916, NIGP01000791, NIGP01000760, NIGP01001028, NIGP01000124, NIGP01001612, NIGP01002055, NIGP01000212, NIGP01001898, NIGP01000149, NIGP01002044, NIGP01000904, NIGP01000123, NIGP01001697, NIGP01001567, NIGP01001956, NIGP01000232, NIGP01002275, NIGP01000142, NIGP01000413, NIGP01001736, NIGP01000728, NIGP01000608, NIGP01000290, NIGP01000477, NIGP01000806, NIGP01000315, NIGP01001858, NIGP01000577, NIGP01001066, NIGP01001934, NIGP01001767, NIGP01000573, NIGP01000648, NIGP01000747, NIGP01000397, NIGP01002103, NIGP01000600, NIGP01002121, NIGP01000254, NIGP01001977, NIGP01000959, NIGP01000009, NIGP01000640, NIGP01001060, NIGP01002278, NIGP01001893, NIGP01000218, NIGP01000148, NIGP01000711, NIGP01001875, NIGP01001085, NIGP01001536, NIGP01001672, NIGP01000736, NIGP01000281, NIGP01000031, NIGP01001758, NIGP01000840, NIGP01001516, NIGP01001961, NIGP01001925, NIGP01001554, NIGP01001606, NIGP01000673, NIGP01001764, NIGP01002054, NIGP01000098, NIGP01000457, NIGP01002095, NIGP01001690, NIGP01001534, NIGP01001942, NIGP01000216, NIGP01000328, NIGP01001909, NIGP01001392, NIGP01001058, NIGP01000512, NIGP01000522, NIGP01000213, NIGP01000464, NIGP01000456, NIGP01001540, NIGP01002260, NIGP01001061, NIGP01002191, NIGP01002064, NIGP01000486, NIGP01000775, NIGP01001847, NIGP01001688, NIGP01001950, NIGP01000963, NIGP01002181, NIGP01002014, NIGP01000424, NIGP01002179, NIGP01001077, NIGP01000870, NIGP01000056, NIGP01001498, NIGP01000639, NIGP01000768, NIGP01000745, NIGP01001781, NIGP01000813, NIGP01000666, NIGP01000087, NIGP01002099, NIGP01000092, NIGP01000885, NIGP01000700, NIGP01001634, NIGP01000381, NIGP01000645, NIGP01000958, NIGP01000620, NIGP01000263, NIGP01000896, NIGP01000025, NIGP01000378, NIGP01000403, NIGP01001639, NIGP01000185, NIGP01001561, NIGP01001601, NIGP01002009, NIGP01000095, NIGP01001704, NIGP01000217, NIGP01001053, NIGP01000194, NIGP01000866, NIGP01001497, NIGP01002126, NIGP01000020, NIGP01001573, NIGP01000291, NIGP01002170, NIGP01001114, NIGP01000289, NIGP01001683, NIGP01002096, NIGP01002167, NIGP01000257, NIGP01000670, NIGP01001810, NIGP01000636, NIGP01000476, NIGP01001928, NIGP01001082, NIGP01000950, NIGP01000759, NIGP01001635, NIGP01000737, NIGP01001415, NIGP01000060, NIGP01002207, NIGP01002077, NIGP01000386, NIGP01000052, NIGP01000121, NIGP01000113, NIGP01000144, NIGP01002154, NIGP01000190, NIGP01002157, NIGP01000269, NIGP01001072, NIGP01000088, NIGP01000583, NIGP01000426, NIGP01002163, NIGP01000581, NIGP01000125, NIGP01000247, NIGP01001791, NIGP01001499, NIGP01001676, NIGP01001711, NIGP01001902, NIGP01000523, NIGP01001870, NIGP01001035, NIGP01000709, NIGP01001763, NIGP01000367, NIGP01000597, NIGP01001068, NIGP01002146, NIGP01000473, NIGP01001748, NIGP01001728, NIGP01000823, NIGP01000103, NIGP01002106, NIGP01000014, NIGP01000134, NIGP01002065, NIGP01000203, NIGP01002263, NIGP01001737, NIGP01001819, NIGP01002151, NIGP01001833, NIGP01000969, NIGP01002273, NIGP01001059, NIGP01002283, NIGP01001807, NIGP01000375, NIGP01000507, NIGP01000714, NIGP01001880, NIGP01000852, NIGP01000348, NIGP01002042, NIGP01000344, NIGP01000489, NIGP01000757, NIGP01000340, NIGP01000447, NIGP01001805, NIGP01000374, NIGP01000713, NIGP01000069, NIGP01002122, NIGP01000734, NIGP01000047, NIGP01001958, NIGP01001890, NIGP01000453, NIGP01001994, NIGP01000805, NIGP01001749, NIGP01002180, NIGP01001979, NIGP01000621, NIGP01000694, NIGP01000972, NIGP01001968, NIGP01001839, NIGP01000449, NIGP01001989, NIGP01001960, NIGP01000209, NIGP01000156, NIGP01002001, NIGP01000150, NIGP01000991, NIGP01000514, NIGP01000871, NIGP01001440, NIGP01000157, NIGP01001842, NIGP01000285, NIGP01001281, NIGP01001572, NIGP01000786, NIGP01001867, NIGP01002158, NIGP01001521, NIGP01000084, NIGP01002086, NIGP01001517, NIGP01002189, NIGP01000919, NIGP01001530, NIGP01000635, NIGP01000107, NIGP01000204, NIGP01001785, NIGP01000644, NIGP01001014, NIGP01000228, NIGP01002264, NIGP01000557, NIGP01000329, NIGP01000539, NIGP01001630, NIGP01001049, NIGP01002110, NIGP01002128, NIGP01001439, NIGP01002101, NIGP01002129, NIGP01001952, NIGP01000999, NIGP01000411, NIGP01000750, NIGP01000096, NIGP01001811, NIGP01002308, NIGP01000718, NIGP01002193, NIGP01001047, NIGP01000938, NIGP01000053, NIGP01001041, NIGP01001595, NIGP01001752, NIGP01000547, NIGP01000710, NIGP01002288, NIGP01002177, NIGP01001533, NIGP01001838, NIGP01002186, NIGP01001691, NIGP01001301, NIGP01000667, NIGP01000617, NIGP01000441, NIGP01001240, NIGP01001991, NIGP01001046, NIGP01000041, NIGP01002130, NIGP01000633, NIGP01000907, NIGP01001018, NIGP01001519, NIGP01000017, NIGP01001217, NIGP01000654, NIGP01001795, NIGP01000422, NIGP01000967, NIGP01000942, NIGP01000609, NIGP01000428, NIGP01000560, NIGP01000401, NIGP01001081, NIGP01000177, NIGP01000882, NIGP01001067, NIGP01000326, NIGP01000843, NIGP01002118, NIGP01000663, NIGP01000310, NIGP01000233, NIGP01001828, NIGP01000465, NIGP01000953, NIGP01000649, NIGP01002298, NIGP01000394, NIGP01001743, NIGP01001558, NIGP01000377, NIGP01000970, NIGP01

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': NIGP01000990
##   - in 'y': NIGP01002089, NIGP01000727, NIGP01000475, NIGP01002221, NIGP01001492, NIGP01000892, NIGP01000201, NIGP01001727, NIGP01001982, NIGP01000101, NIGP01002078, NIGP01001086, NIGP01002082, NIGP01002045, NIGP01002203, NIGP01000451, NIGP01000495, NIGP01002020, NIGP01001844, NIGP01002286, NIGP01002127, NIGP01000184, NIGP01000944, NIGP01000304, NIGP01000130, NIGP01001935, NIGP01000647, NIGP01002035, NIGP01001914, NIGP01001774, NIGP01000058, NIGP01000662, NIGP01000976, NIGP01000253, NIGP01001770, NIGP01000416, NIGP01001671, NIGP01001712, NIGP01002113, NIGP01001514, NIGP01000379, NIGP01000036, NIGP01002034, NIGP01000552, NIGP01001837, NIGP01001551, NIGP01000525, NIGP01002215, NIGP01001678, NIGP01000638, NIGP01001599, NIGP01000106, NIGP01001294, NIGP01002178, NIGP01000256, NIGP01000283, NIGP01001031, NIGP01002155, NIGP01000077, NIGP01001793, NIGP01000371, NIGP01000658, NIGP01001480, NIGP01000848, NIGP01000415, NIGP01000180, NIGP01001039, NIGP01000110, NIGP01000242, NIGP01001503, NIGP01001976, NIGP01000537, NIGP01000565, NIGP01000807, NIGP01002168, NIGP01000593, NIGP01000482, NIGP01002289, NIGP01000751, NIGP01001945, NIGP01000574, NIGP01002209, NIGP01001759, NIGP01000402, NIGP01000198, NIGP01000432, NIGP01002029, NIGP01000294, NIGP01000909, NIGP01000139, NIGP01000282, NIGP01001786, NIGP01000376, NIGP01001698, NIGP01001206, NIGP01002240, NIGP01001030, NIGP01001414, NIGP01001750, NIGP01002188, NIGP01000072, NIGP01000080, NIGP01002269, NIGP01000033, NIGP01001661, NIGP01002234, NIGP01000602, NIGP01000761, NIGP01000063, NIGP01002251, NIGP01002176, NIGP01000433, NIGP01000034, NIGP01000159, NIGP01002300, NIGP01001458, NIGP01001507, NIGP01000182, NIGP01000941, NIGP01000188, NIGP01002297, NIGP01000697, NIGP01000629, NIGP01001062, NIGP01001508, NIGP01002230, NIGP01000197, NIGP01000266, NIGP01000699, NIGP01000541, NIGP01001755, NIGP01001696, NIGP01000656, NIGP01000563, NIGP01000888, NIGP01000327, NIGP01001988, NIGP01001641, NIGP01001846, NIGP01001908, NIGP01000986, NIGP01001769, NIGP01000440, NIGP01002046, NIGP01000505, NIGP01002152, NIGP01000627, NIGP01000598, NIGP01000274, NIGP01000414, NIGP01002253, NIGP01001029, NIGP01000599, NIGP01001510, NIGP01001887, NIGP01000650, NIGP01000735, NIGP01002199, NIGP01001036, NIGP01002153, NIGP01001949, NIGP01002196, NIGP01000407, NIGP01001919, NIGP01000809, NIGP01001929, NIGP01001703, NIGP01001866, NIGP01002058, NIGP01000779, NIGP01001557, NIGP01002024, NIGP01000859, NIGP01000206, NIGP01000189, NIGP01000210, NIGP01001019, NIGP01001717, NIGP01002087, NIGP01001650, NIGP01001965, NIGP01001845, NIGP01000361, NIGP01000579, NIGP01001741, NIGP01000205, NIGP01000802, NIGP01001757, NIGP01000356, NIGP01000893, NIGP01000637, NIGP01001469, NIGP01000780, NIGP01001915, NIGP01001943, NIGP01000335, NIGP01001933, NIGP01000920, NIGP01000863, NIGP01000417, NIGP01000845, NIGP01001008, NIGP01000039, NIGP01001816, NIGP01000665, NIGP01000818, NIGP01000521, NIGP01000578, NIGP01000532, NIGP01000821, NIGP01001546, NIGP01002242, NIGP01000384, NIGP01000295, NIGP01000408, NIGP01001940, NIGP01001566, NIGP01000865, NIGP01000187, NIGP01000962, NIGP01000316, NIGP01001024, NIGP01001076, NIGP01000497, NIGP01000916, NIGP01001927, NIGP01000791, NIGP01000124, NIGP01001612, NIGP01002055, NIGP01000212, NIGP01001898, NIGP01002044, NIGP01000363, NIGP01000904, NIGP01002133, NIGP01000123, NIGP01001697, NIGP01001567, NIGP01001956, NIGP01002275, NIGP01000142, NIGP01000413, NIGP01001736, NIGP01000728, NIGP01000290, NIGP01000477, NIGP01000806, NIGP01000315, NIGP01001858, NIGP01000577, NIGP01001066, NIGP01001934, NIGP01001767, NIGP01000648, NIGP01000747, NIGP01000397, NIGP01002103, NIGP01000600, NIGP01002121, NIGP01000254, NIGP01001977, NIGP01000959, NIGP01000009, NIGP01000640, NIGP01000061, NIGP01001893, NIGP01000218, NIGP01000711, NIGP01001875, NIGP01001085, NIGP01000463, NIGP01001672, NIGP01000450, NIGP01000281, NIGP01000031, NIGP01001758, NIGP01000840, NIGP01001961, NIGP01001925, NIGP01001554, NIGP01001606, NIGP01001764, NIGP01002054, NIGP01000098, NIGP01000457, NIGP01002095, NIGP01001690, NIGP01001534, NIGP01001942, NIGP01000216, NIGP01000965, NIGP01000328, NIGP01001909, NIGP01001392, NIGP01001058, NIGP01000512, NIGP01000213, NIGP01001593, NIGP01000464, NIGP01000456, NIGP01001540, NIGP01002260, NIGP01000279, NIGP01001061, NIGP01002064, NIGP01000775, NIGP01001847, NIGP01001950, NIGP01000963, NIGP01002181, NIGP01000424, NIGP01002179, NIGP01001077, NIGP01000870, NIGP01000580, NIGP01000056, NIGP01001498, NIGP01000639, NIGP01000768, NIGP01000745, NIGP01001781, NIGP01000666, NIGP01000087, NIGP01002099, NIGP01000092, NIGP01000885, NIGP01000700, NIGP01001634, NIGP01000381, NIGP01000645, NIGP01000958, NIGP01000263, NIGP01000896, NIGP01000046, NIGP01000378, NIGP01000403, NIGP01001639, NIGP01001561, NIGP01002009, NIGP01000095, NIGP01001704, NIGP01000217, NIGP01001053, NIGP01000194, NIGP01000866, NIGP01001497, NIGP01002126, NIGP01001573, NIGP01001114, NIGP01000289, NIGP01002096, NIGP01002167, NIGP01000257, NIGP01000996, NIGP01000670, NIGP01001810, NIGP01000476, NIGP01001928, NIGP01001082, NIGP01000950, NIGP01000759, NIGP01001635, NIGP01000737, NIGP01001415, NIGP01000060, NIGP01002207, NIGP01002077, NIGP01000386, NIGP01000052, NIGP01000121, NIGP01000113, NIGP01000144, NIGP01002157, NIGP01000269, NIGP01000088, NIGP01000583, NIGP01000426, NIGP01000167, NIGP01002163, NIGP01000581, NIGP01000125, NIGP01000247, NIGP01001791, NIGP01001499, NIGP01001676, NIGP01001711, NIGP01001902, NIGP01000523, NIGP01000480, NIGP01001870, NIGP01000709, NIGP01000367, NIGP01001068, NIGP01002146, NIGP01000473, NIGP01001748, NIGP01001728, NIGP01000823, NIGP01002106, NIGP01000014, NIGP01000134, NIGP01002065, NIGP01000203, NIGP01000657, NIGP01002263, NIGP01001737, NIGP01001819, NIGP01002151, NIGP01001833, NIGP01000969, NIGP01001059, NIGP01000596, NIGP01001807, NIGP01000375, NIGP01000507, NIGP01000714, NIGP01001880, NIGP01002042, NIGP01000344, NIGP01000489, NIGP01000757, NIGP01000447, NIGP01001805, NIGP01000374, NIGP01000713, NIGP01002122, NIGP01000734, NIGP01000047, NIGP01001958, NIGP01000453, NIGP01000805, NIGP01001749, NIGP01002180, NIGP01001979, NIGP01000621, NIGP01000694, NIGP01000972, NIGP01001968, NIGP01001839, NIGP01001989, NIGP01001960, NIGP01000209, NIGP01002187, NIGP01000156, NIGP01002001, NIGP01001813, NIGP01000150, NIGP01000991, NIGP01002084, NIGP01000514, NIGP01002039, NIGP01000871, NIGP01001440, NIGP01001739, NIGP01001713, NIGP01000157, NIGP01001842, NIGP01001073, NIGP01000005, NIGP01000285, NIGP01001572, NIGP01000786, NIGP01001867, NIGP01001521, NIGP01000084, NIGP01002086, NIGP01001338, NIGP01001517, NIGP01000919, NIGP01000635, NIGP01000107, NIGP01001785, NIGP01001014, NIGP01002228, NIGP01000228, NIGP01002264, NIGP01000329, NIGP01000539, NIGP01001630, NIGP01001049, NIGP01002110, NIGP01002128, NIGP01001439, NIGP01002101, NIGP01002129, NIGP01001952, NIGP01000411, NIGP01001146, NIGP01001074, NIGP01000750, NIGP01000096, NIGP01001811, NIGP01000718, NIGP01002193, NIGP01000938, NIGP01000053, NIGP01001041, NIGP01001595, NIGP01001752, NIGP01000547, NIGP01000710, NIGP01002288, NIGP01002177, NIGP01001533, NIGP01001838, NIGP01001691, NIGP01001301, NIGP01000667, NIGP01000617, NIGP01000441, NIGP01001240, NIGP01001991, NIGP01001046, NIGP01000041, NIGP01002130, NIGP01000633, NIGP01000907, NIGP01001018, NIGP01001519, NIGP01001821, NIGP01001153, NIGP01001217, NIGP01000654, NIGP01001795, NIGP01000422, NIGP01000967, NIGP01000942, NIGP01000609, NIGP01000560, NIGP01000401, NIGP01001081, NIGP01000652, NIGP01000055, NIGP01000177, NIGP01000882, NIGP01001067, NIGP01000326, NIGP01002229, NIGP01000616, NIGP01000238, NIGP01000742, NIGP01000843, NIGP01002118, NIGP01001178, NIGP01000310, NIGP01000979, NIGP01000233, NIGP01000465, NIGP01000953, NIGP01000649, NIGP01001993, NIGP01002298, NIGP01001743, NIGP01001558, NIGP01000377, NIGP01000970, NIGP01000948, NIGP01001216, NIGP01000436, NIGP01000715, NIGP01000261, NIGP01001901, NIGP01000481, NIGP01000674, NIGP01001777, NIGP01000877, NIGP01000632, NIGP01000546, NIGP01000752, NIGP01000010, NIGP01000421, NIGP01000501, NIGP01000082, NIGP01000089, NIGP01001897, NIGP01001710, NIGP01

countmat <- do.call(cbind,countmat)
colnames(countmat) <- basename(unlist(beds))

#now bind nGRSet, a GRanges with peak ranges and TRUE/FALSE at each peak, with countmat, the number of reads at each peak
mcols(nGRSet) <- cbind(as.data.frame(mcols(nGRSet)),countmat)

#you can convert this GRanges object to a dataframe
peaksDF <- as.data.frame(nGRSet)
peaksDF$peakID <- paste0(peaksDF$seqnames, ":", peaksDF$start, "_", peaksDF$end, ":", peaksDF$strand)
head(peaksDF)

##   seqnames   start     end width strand
## 1        1  301043  301053    11      +
## 2        1  580903  580913    11      +
## 3        1 1183109 1183119    11      +
## 4        1 1386212 1386222    11      +
## 5        1 1947557 1947569    13      +
## 6        1 1947625 1947635    11      +
##   KRG091819_S1_L001_R1_001_collapse_rm5_Aag2_Ago1_Exp6A_trim_clip.peaks.txt
## 1                                                                     FALSE
## 2                                                                     FALSE
## 3                                                                     FALSE
## 4                                                                      TRUE
## 5                                                                     FALSE
## 6                                                                      TRUE
##   KRG091819_S1_L001_R1_001_collapse_rm5_Aag2_Ago1_Exp6B_trim_clip.peaks.txt
## 1                                                                     FALSE
## 2                                                                     FALSE
## 3                                                                     FALSE
## 4                                                                     FALSE
## 5                                                                      TRUE
## 6                                                                     FALSE
##   KRG092419_S1_L001_R1_001_collapse_Aag2_Ago1_Exp7A_rm5_clip.peaks.txt
## 1                                                                FALSE
## 2                                                                 TRUE
## 3                                                                 TRUE
## 4                                                                FALSE
## 5                                                                FALSE
## 6                                                                FALSE
##   KRG092419_S1_L001_R1_001_collapse_Aag2_Ago1_Exp7B_rm5_clip.peaks.txt
## 1                                                                 TRUE
## 2                                                                FALSE
## 3                                                                FALSE
## 4                                                                FALSE
## 5                                                                 TRUE
## 6                                                                FALSE
##   KRG091819_S1_L001_R1_001_collapse_rm5_Aag2_Ago1_Exp6A_trim_clip.bed
## 1                                                                   0
## 2                                                                   0
## 3                                                                   0
## 4                                                                   3
## 5                                                                   3
## 6                                                                   3
##   KRG091819_S1_L001_R1_001_collapse_rm5_Aag2_Ago1_Exp6B_trim_clip.bed
## 1                                                                   0
## 2                                                                   0
## 3                                                                   0
## 4                                                                   1
## 5                                                                   4
## 6                                                                   1
##   KRG092419_S1_L001_R1_001_collapse_Aag2_Ago1_Exp7A_rm5_clip.bed
## 1                                                              0
## 2                                                              3
## 3                                                              3
## 4                                                              0
## 5                                                              5
## 6                                                              2
##   KRG092419_S1_L001_R1_001_collapse_Aag2_Ago1_Exp7B_rm5_clip.bed
## 1                                                              3
## 2                                                              0
## 3                                                              3
## 4                                                              0
## 5                                                              5
## 6                                                              0
##                peakID
## 1   1:301043_301053:+
## 2   1:580903_580913:+
## 3 1:1183109_1183119:+
## 4 1:1386212_1386222:+
## 5 1:1947557_1947569:+
## 6 1:1947625_1947635:+

now you have your count matrix!

you can perform operations on sample groups to filter, visualize data, annotate your peaks, and more...

For example, if you are dealing with a custom genome without pre-built genomes and annotation, you can still easily annotate your peaks
Here we provide an example using ChIPseeker, which you can also use to visualize genomic annotation (see ChIPseeker vignette for alternate visualizations)

#load required packages
library(ChIPseeker)
library(GenomicFeatures)

gtffile <- "/Users/kathryn/Aedes-aegypti-LVP_AGWG_BASEFEATURES_AaegL5.2.gtf"  #custom gtf or gff

TxDb <- makeTxDbFromGFF(gtffile)

## Import genomic features from the file as a GRanges object ... OK
## Prepare the 'metadata' data frame ... OK
## Make the TxDb object ...

## Warning in .get_cds_IDX(type, phase): The "phase" metadata column contains non-NA values for features of
##   type stop_codon. This information was ignored.

## OK

allanno <- annotatePeak(nGRSet,
                              TxDb=TxDb,
                              sameStrand=FALSE,
                              genomicAnnotationPriority = c("3UTR", "5UTR", "Exon",
                                                            "Intron", "Promoter", "Downstream", "Intergenic"),
                              overlap = "all")

## >> preparing features information...      2021-03-16 02:33:31 
## >> identifying nearest features...        2021-03-16 02:33:31

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': NIGP01000081, NIGP01000723, NIGP01001312, NIGP01001552, NIGP01001579, NIGP01001581, NIGP01001642, NIGP01001658, NIGP01001735, NIGP01001852, NIGP01002067, NIGP01000332, NIGP01000588, NIGP01001651, NIGP01001665, NIGP01001990, NIGP01000226, NIGP01000358, NIGP01000825, NIGP01000917, NIGP01000946, NIGP01001002, NIGP01001056, NIGP01001101, NIGP01001349, NIGP01001814, NIGP01002025, NIGP01001900
##   - in 'y': NIGP01000006, NIGP01000009, NIGP01000010, NIGP01000015, NIGP01000025, NIGP01000028, NIGP01000033, NIGP01000036, NIGP01000043, NIGP01000049, NIGP01000051, NIGP01000052, NIGP01000055, NIGP01000056, NIGP01000062, NIGP01000063, NIGP01000064, NIGP01000073, NIGP01000075, NIGP01000076, NIGP01000077, NIGP01000079, NIGP01000080, NIGP01000083, NIGP01000087, NIGP01000094, NIGP01000096, NIGP01000101, NIGP01000102, NIGP01000104, NIGP01000106, NIGP01000107, NIGP01000110, NIGP01000115, NIGP01000116, NIGP01000117, NIGP01000121, NIGP01000123, NIGP01000124, NIGP01000125, NIGP01000129, NIGP01000130, NIGP01000133, NIGP01000134, NIGP01000137, NIGP01000139, NIGP01000144, NIGP01000149, NIGP01000156, NIGP01000158, NIGP01000159, NIGP01000172, NIGP01000177, NIGP01000180, NIGP01000183, NIGP01000184, NIGP01000185, NIGP01000186, NIGP01000187, NIGP01000188, NIGP01000189, NIGP01000197, NIGP01000198, NIGP01000200, NIGP01000201, NIGP01000203, NIGP01000204, NIGP01000205, NIGP01000206, NIGP01000207, NIGP01000210, NIGP01000212, NIGP01000213, NIGP01000216, NIGP01000218, NIGP01000220, NIGP01000221, NIGP01000222, NIGP01000223, NIGP01000225, NIGP01000228, NIGP01000230, NIGP01000236, NIGP01000238, NIGP01000239, NIGP01000240, NIGP01000244, NIGP01000247, NIGP01000248, NIGP01000250, NIGP01000253, NIGP01000254, NIGP01000256, NIGP01000257, NIGP01000262, NIGP01000263, NIGP01000265, NIGP01000267, NIGP01000270, NIGP01000280, NIGP01000281, NIGP01000288, NIGP01000290, NIGP01000292, NIGP01000294, NIGP01000295, NIGP01000297, NIGP01000298, NIGP01000309, NIGP01000310, NIGP01000312, NIGP01000315, NIGP01000319, NIGP01000324, NIGP01000325, NIGP01000329, NIGP01000330, NIGP01000345, NIGP01000349, NIGP01000351, NIGP01000352, NIGP01000356, NIGP01000357, NIGP01000359, NIGP01000363, NIGP01000365, NIGP01000371, NIGP01000374, NIGP01000375, NIGP01000376, NIGP01000377, NIGP01000379, NIGP01000383, NIGP01000386, NIGP01000396, NIGP01000397, NIGP01000407, NIGP01000410, NIGP01000412, NIGP01000413, NIGP01000415, NIGP01000417, NIGP01000421, NIGP01000422, NIGP01000424, NIGP01000428, NIGP01000430, NIGP01000432, NIGP01000434, NIGP01000437, NIGP01000440, NIGP01000441, NIGP01000445, NIGP01000451, NIGP01000452, NIGP01000461, NIGP01000463, NIGP01000465, NIGP01000466, NIGP01000475, NIGP01000481, NIGP01000482, NIGP01000489, NIGP01000490, NIGP01000495, NIGP01000497, NIGP01000501, NIGP01000507, NIGP01000514, NIGP01000515, NIGP01000518, NIGP01000519, NIGP01000520, NIGP01000521, NIGP01000524, NIGP01000525, NIGP01000530, NIGP01000531, NIGP01000532, NIGP01000535, NIGP01000536, NIGP01000537, NIGP01000539, NIGP01000541, NIGP01000552, NIGP01000553, NIGP01000556, NIGP01000557, NIGP01000560, NIGP01000561, NIGP01000566, NIGP01000569, NIGP01000570, NIGP01000571, NIGP01000573, NIGP01000574, NIGP01000579, NIGP01000590, NIGP01000591, NIGP01000596, NIGP01000598, NIGP01000599, NIGP01000600, NIGP01000601, NIGP01000602, NIGP01000604, NIGP01000608, NIGP01000610, NIGP01000612, NIGP01000622, NIGP01000627, NIGP01000630, NIGP01000633, NIGP01000634, NIGP01000635, NIGP01000639, NIGP01000640, NIGP01000648, NIGP01000649, NIGP01000650, NIGP01000651, NIGP01000657, NIGP01000658, NIGP01000660, NIGP01000662, NIGP01000665, NIGP01000666, NIGP01000667, NIGP01000669, NIGP01000673, NIGP01000676, NIGP01000681, NIGP01000684, NIGP01000686, NIGP01000687, NIGP01000690, NIGP01000692, NIGP01000695, NIGP01000699, NIGP01000702, NIGP01000703, NIGP01000706, NIGP01000709, NIGP01000710, NIGP01000712, NIGP01000714, NIGP01000715, NIGP01000716, NIGP01000718, NIGP01000721, NIGP01000724, NIGP01000727, NIGP01000730, NIGP01000734, NIGP01000737, NIGP01000740, NIGP01000745, NIGP01000751, NIGP01000754, NIGP01000756, NIGP01000760, NIGP01000761, NIGP01000775, NIGP01000778, NIGP01000779, NIGP01000781, NIGP01000782, NIGP01000783, NIGP01000791, NIGP01000799, NIGP01000802, NIGP01000806, NIGP01000807, NIGP01000811, NIGP01000812, NIGP01000813, NIGP01000818, NIGP01000821, NIGP01000822, NIGP01000823, NIGP01000826, NIGP01000827, NIGP01000835, NIGP01000843, NIGP01000846, NIGP01000847, NIGP01000848, NIGP01000849, NIGP01000850, NIGP01000856, NIGP01000859, NIGP01000860, NIGP01000861, NIGP01000867, NIGP01000870, NIGP01000882, NIGP01000883, NIGP01000885, NIGP01000892, NIGP01000896, NIGP01000900, NIGP01000904, NIGP01000905, NIGP01000906, NIGP01000910, NIGP01000915, NIGP01000920, NIGP01000921, NIGP01000923, NIGP01000929, NIGP01000932, NIGP01000937, NIGP01000938, NIGP01000939, NIGP01000941, NIGP01000942, NIGP01000944, NIGP01000947, NIGP01000948, NIGP01000952, NIGP01000954, NIGP01000957, NIGP01000958, NIGP01000959, NIGP01000960, NIGP01000976, NIGP01000977, NIGP01000978, NIGP01000980, NIGP01000983, NIGP01000986, NIGP01000991, NIGP01000996, NIGP01001003, NIGP01001006, NIGP01001008, NIGP01001010, NIGP01001013, NIGP01001015, NIGP01001018, NIGP01001022, NIGP01001023, NIGP01001024, NIGP01001031, NIGP01001032, NIGP01001035, NIGP01001039, NIGP01001041, NIGP01001043, NIGP01001046, NIGP01001047, NIGP01001053, NIGP01001055, NIGP01001057, NIGP01001059, NIGP01001061, NIGP01001068, NIGP01001070, NIGP01001072, NIGP01001074, NIGP01001075, NIGP01001081, NIGP01001082, NIGP01001083, NIGP01001085, NIGP01001086, NIGP01001092, NIGP01001097, NIGP01001100, NIGP01001102, NIGP01001108, NIGP01001110, NIGP01001119, NIGP01001126, NIGP01001136, NIGP01001165, NIGP01001173, NIGP01001180, NIGP01001185, NIGP01001186, NIGP01001196, NIGP01001197, NIGP01001208, NIGP01001211, NIGP01001214, NIGP01001216, NIGP01001230, NIGP01001233, NIGP01001237, NIGP01001238, NIGP01001240, NIGP01001243, NIGP01001247, NIGP01001249, NIGP01001254, NIGP01001255, NIGP01001256, NIGP01001262, NIGP01001263, NIGP01001282, NIGP01001285, NIGP01001287, NIGP01001295, NIGP01001296, NIGP01001297, NIGP01001301, NIGP01001311, NIGP01001322, NIGP01001325, NIGP01001329, NIGP01001335, NIGP01001341, NIGP01001343, NIGP01001348, NIGP01001350, NIGP01001352, NIGP01001353, NIGP01001355, NIGP01001363, NIGP01001365, NIGP01001372, NIGP01001373, NIGP01001374, NIGP01001377, NIGP01001382, NIGP01001386, NIGP01001397, NIGP01001398, NIGP01001407, NIGP01001408, NIGP01001414, NIGP01001415, NIGP01001416, NIGP01001417, NIGP01001426, NIGP01001431, NIGP01001438, NIGP01001442, NIGP01001450, NIGP01001455, NIGP01001458, NIGP01001463, NIGP01001464, NIGP01001468, NIGP01001469, NIGP01001476, NIGP01001477, NIGP01001478, NIGP01001480, NIGP01001482, NIGP01001497, NIGP01001501, NIGP01001506, NIGP01001507, NIGP01001509, NIGP01001516, NIGP01001519, NIGP01001520, NIGP01001522, NIGP01001530, NIGP01001531, NIGP01001534, NIGP01001536, NIGP01001546, NIGP01001547, NIGP01001549, NIGP01001551, NIGP01001553, NIGP01001557, NIGP01001562, NIGP01001568, NIGP01001572, NIGP01001573, NIGP01001574, NIGP01001575, NIGP01001576, NIGP01001578, NIGP01001580, NIGP01001587, NIGP01001589, NIGP01001591, NIGP01001593, NIGP01001597, NIGP01001599, NIGP01001603, NIGP01001614, NIGP01001615, NIGP01001617, NIGP01001618, NIGP01001622, NIGP01001624, NIGP01001630, NIGP01001639, NIGP01001640, NIGP01001641, NIGP01001645, NIGP01001646, NIGP01001648, NIGP01001661, NIGP01001671, NIGP01001672, NIGP01001675, NIGP01001676, NIGP01001678, NIGP01001682, NIGP01001690, NIGP01001692, NIGP01001696, NIGP01001699, NIGP01001702, NIGP01001703, NIGP01001705, NIGP01001706, NIGP01001711, NIGP01001712, NIGP01001713, NIGP01001717, NIGP01001719, NIGP01001726, NIGP01001727, NIGP01001728, NIGP01001729, NIGP01001730, NIGP01001732, NIGP01001736, NIGP01001738, NIGP01001743, NIGP01001749, NIGP01001750, NIGP01001752, NIGP01001755, NIGP01001756, NIGP01001758, NIGP01001766, NIGP01001767, NIGP01001769, NIGP01001770, NIGP01001774, NIGP01001784, NIGP01001786, NIGP01001788, NIGP01001789, NIGP01001800, NIGP01001801, NIGP01001810, NIGP01001811, NIGP01001816, NIGP01001817, NIGP01001818, NIGP01001819, NIGP01

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': NIGP01000081, NIGP01000723, NIGP01001312, NIGP01001552, NIGP01001579, NIGP01001581, NIGP01001642, NIGP01001658, NIGP01001735, NIGP01001852, NIGP01002067, NIGP01000332, NIGP01000588, NIGP01001651, NIGP01001665, NIGP01001990, NIGP01000226, NIGP01000358, NIGP01000825, NIGP01000917, NIGP01000946, NIGP01001002, NIGP01001056, NIGP01001101, NIGP01001349, NIGP01001814, NIGP01002025, NIGP01001900
##   - in 'y': NIGP01000006, NIGP01000009, NIGP01000010, NIGP01000015, NIGP01000025, NIGP01000028, NIGP01000033, NIGP01000036, NIGP01000043, NIGP01000049, NIGP01000051, NIGP01000052, NIGP01000055, NIGP01000056, NIGP01000062, NIGP01000063, NIGP01000064, NIGP01000073, NIGP01000075, NIGP01000076, NIGP01000077, NIGP01000079, NIGP01000080, NIGP01000083, NIGP01000087, NIGP01000094, NIGP01000096, NIGP01000101, NIGP01000102, NIGP01000104, NIGP01000106, NIGP01000107, NIGP01000110, NIGP01000115, NIGP01000116, NIGP01000117, NIGP01000121, NIGP01000123, NIGP01000124, NIGP01000125, NIGP01000129, NIGP01000130, NIGP01000133, NIGP01000134, NIGP01000137, NIGP01000139, NIGP01000144, NIGP01000149, NIGP01000156, NIGP01000158, NIGP01000159, NIGP01000172, NIGP01000177, NIGP01000180, NIGP01000183, NIGP01000184, NIGP01000185, NIGP01000186, NIGP01000187, NIGP01000188, NIGP01000189, NIGP01000197, NIGP01000198, NIGP01000200, NIGP01000201, NIGP01000203, NIGP01000204, NIGP01000205, NIGP01000206, NIGP01000207, NIGP01000210, NIGP01000212, NIGP01000213, NIGP01000216, NIGP01000218, NIGP01000220, NIGP01000221, NIGP01000222, NIGP01000223, NIGP01000225, NIGP01000228, NIGP01000230, NIGP01000236, NIGP01000238, NIGP01000239, NIGP01000240, NIGP01000244, NIGP01000247, NIGP01000248, NIGP01000250, NIGP01000253, NIGP01000254, NIGP01000256, NIGP01000257, NIGP01000262, NIGP01000263, NIGP01000265, NIGP01000267, NIGP01000270, NIGP01000280, NIGP01000281, NIGP01000288, NIGP01000290, NIGP01000292, NIGP01000294, NIGP01000295, NIGP01000297, NIGP01000298, NIGP01000309, NIGP01000310, NIGP01000312, NIGP01000315, NIGP01000319, NIGP01000324, NIGP01000325, NIGP01000329, NIGP01000330, NIGP01000345, NIGP01000349, NIGP01000351, NIGP01000352, NIGP01000356, NIGP01000357, NIGP01000359, NIGP01000363, NIGP01000365, NIGP01000371, NIGP01000374, NIGP01000375, NIGP01000376, NIGP01000377, NIGP01000379, NIGP01000383, NIGP01000386, NIGP01000396, NIGP01000397, NIGP01000407, NIGP01000410, NIGP01000412, NIGP01000413, NIGP01000415, NIGP01000417, NIGP01000421, NIGP01000422, NIGP01000424, NIGP01000428, NIGP01000430, NIGP01000432, NIGP01000434, NIGP01000437, NIGP01000440, NIGP01000441, NIGP01000445, NIGP01000451, NIGP01000452, NIGP01000461, NIGP01000463, NIGP01000465, NIGP01000466, NIGP01000475, NIGP01000481, NIGP01000482, NIGP01000489, NIGP01000490, NIGP01000495, NIGP01000497, NIGP01000501, NIGP01000507, NIGP01000514, NIGP01000515, NIGP01000518, NIGP01000519, NIGP01000520, NIGP01000521, NIGP01000524, NIGP01000525, NIGP01000530, NIGP01000531, NIGP01000532, NIGP01000535, NIGP01000536, NIGP01000537, NIGP01000539, NIGP01000541, NIGP01000552, NIGP01000553, NIGP01000556, NIGP01000557, NIGP01000560, NIGP01000561, NIGP01000566, NIGP01000569, NIGP01000570, NIGP01000571, NIGP01000573, NIGP01000574, NIGP01000579, NIGP01000590, NIGP01000591, NIGP01000596, NIGP01000598, NIGP01000599, NIGP01000600, NIGP01000601, NIGP01000602, NIGP01000604, NIGP01000608, NIGP01000610, NIGP01000612, NIGP01000622, NIGP01000627, NIGP01000630, NIGP01000633, NIGP01000634, NIGP01000635, NIGP01000639, NIGP01000640, NIGP01000648, NIGP01000649, NIGP01000650, NIGP01000651, NIGP01000657, NIGP01000658, NIGP01000660, NIGP01000662, NIGP01000665, NIGP01000666, NIGP01000667, NIGP01000669, NIGP01000673, NIGP01000676, NIGP01000681, NIGP01000684, NIGP01000686, NIGP01000687, NIGP01000690, NIGP01000692, NIGP01000695, NIGP01000699, NIGP01000702, NIGP01000703, NIGP01000706, NIGP01000709, NIGP01000710, NIGP01000712, NIGP01000714, NIGP01000715, NIGP01000716, NIGP01000718, NIGP01000721, NIGP01000724, NIGP01000727, NIGP01000730, NIGP01000734, NIGP01000737, NIGP01000740, NIGP01000745, NIGP01000751, NIGP01000754, NIGP01000756, NIGP01000760, NIGP01000761, NIGP01000775, NIGP01000778, NIGP01000779, NIGP01000781, NIGP01000782, NIGP01000783, NIGP01000791, NIGP01000799, NIGP01000802, NIGP01000806, NIGP01000807, NIGP01000811, NIGP01000812, NIGP01000813, NIGP01000818, NIGP01000821, NIGP01000822, NIGP01000823, NIGP01000826, NIGP01000827, NIGP01000835, NIGP01000843, NIGP01000846, NIGP01000847, NIGP01000848, NIGP01000849, NIGP01000850, NIGP01000856, NIGP01000859, NIGP01000860, NIGP01000861, NIGP01000867, NIGP01000870, NIGP01000882, NIGP01000883, NIGP01000885, NIGP01000892, NIGP01000896, NIGP01000900, NIGP01000904, NIGP01000905, NIGP01000906, NIGP01000910, NIGP01000915, NIGP01000920, NIGP01000921, NIGP01000923, NIGP01000929, NIGP01000932, NIGP01000937, NIGP01000938, NIGP01000939, NIGP01000941, NIGP01000942, NIGP01000944, NIGP01000947, NIGP01000948, NIGP01000952, NIGP01000954, NIGP01000957, NIGP01000958, NIGP01000959, NIGP01000960, NIGP01000976, NIGP01000977, NIGP01000978, NIGP01000980, NIGP01000983, NIGP01000986, NIGP01000991, NIGP01000996, NIGP01001003, NIGP01001006, NIGP01001008, NIGP01001010, NIGP01001013, NIGP01001015, NIGP01001018, NIGP01001022, NIGP01001023, NIGP01001024, NIGP01001031, NIGP01001032, NIGP01001035, NIGP01001039, NIGP01001041, NIGP01001043, NIGP01001046, NIGP01001047, NIGP01001053, NIGP01001055, NIGP01001057, NIGP01001059, NIGP01001061, NIGP01001068, NIGP01001070, NIGP01001072, NIGP01001074, NIGP01001075, NIGP01001081, NIGP01001082, NIGP01001083, NIGP01001085, NIGP01001086, NIGP01001092, NIGP01001097, NIGP01001100, NIGP01001102, NIGP01001108, NIGP01001110, NIGP01001119, NIGP01001126, NIGP01001136, NIGP01001165, NIGP01001173, NIGP01001180, NIGP01001185, NIGP01001186, NIGP01001196, NIGP01001197, NIGP01001208, NIGP01001211, NIGP01001214, NIGP01001216, NIGP01001230, NIGP01001233, NIGP01001237, NIGP01001238, NIGP01001240, NIGP01001243, NIGP01001247, NIGP01001249, NIGP01001254, NIGP01001255, NIGP01001256, NIGP01001262, NIGP01001263, NIGP01001282, NIGP01001285, NIGP01001287, NIGP01001295, NIGP01001296, NIGP01001297, NIGP01001301, NIGP01001311, NIGP01001322, NIGP01001325, NIGP01001329, NIGP01001335, NIGP01001341, NIGP01001343, NIGP01001348, NIGP01001350, NIGP01001352, NIGP01001353, NIGP01001355, NIGP01001363, NIGP01001365, NIGP01001372, NIGP01001373, NIGP01001374, NIGP01001377, NIGP01001382, NIGP01001386, NIGP01001397, NIGP01001398, NIGP01001407, NIGP01001408, NIGP01001414, NIGP01001415, NIGP01001416, NIGP01001417, NIGP01001426, NIGP01001431, NIGP01001438, NIGP01001442, NIGP01001450, NIGP01001455, NIGP01001458, NIGP01001463, NIGP01001464, NIGP01001468, NIGP01001469, NIGP01001476, NIGP01001477, NIGP01001478, NIGP01001480, NIGP01001482, NIGP01001497, NIGP01001501, NIGP01001506, NIGP01001507, NIGP01001509, NIGP01001516, NIGP01001519, NIGP01001520, NIGP01001522, NIGP01001530, NIGP01001531, NIGP01001534, NIGP01001536, NIGP01001546, NIGP01001547, NIGP01001549, NIGP01001551, NIGP01001553, NIGP01001557, NIGP01001562, NIGP01001568, NIGP01001572, NIGP01001573, NIGP01001574, NIGP01001575, NIGP01001576, NIGP01001578, NIGP01001580, NIGP01001587, NIGP01001589, NIGP01001591, NIGP01001593, NIGP01001597, NIGP01001599, NIGP01001603, NIGP01001614, NIGP01001615, NIGP01001617, NIGP01001618, NIGP01001622, NIGP01001624, NIGP01001630, NIGP01001639, NIGP01001640, NIGP01001641, NIGP01001645, NIGP01001646, NIGP01001648, NIGP01001661, NIGP01001671, NIGP01001672, NIGP01001675, NIGP01001676, NIGP01001678, NIGP01001682, NIGP01001690, NIGP01001692, NIGP01001696, NIGP01001699, NIGP01001702, NIGP01001703, NIGP01001705, NIGP01001706, NIGP01001711, NIGP01001712, NIGP01001713, NIGP01001717, NIGP01001719, NIGP01001726, NIGP01001727, NIGP01001728, NIGP01001729, NIGP01001730, NIGP01001732, NIGP01001736, NIGP01001738, NIGP01001743, NIGP01001749, NIGP01001750, NIGP01001752, NIGP01001755, NIGP01001756, NIGP01001758, NIGP01001766, NIGP01001767, NIGP01001769, NIGP01001770, NIGP01001774, NIGP01001784, NIGP01001786, NIGP01001788, NIGP01001789, NIGP01001800, NIGP01001801, NIGP01001810, NIGP01001811, NIGP01001816, NIGP01001817, NIGP01001818, NIGP01001819, NIGP01

## >> calculating distance from peak to TSS...   2021-03-16 02:33:31 
## >> assigning genomic annotation...        2021-03-16 02:33:31

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': NIGP01000081, NIGP01000723, NIGP01001312, NIGP01001552, NIGP01001579, NIGP01001581, NIGP01001642, NIGP01001658, NIGP01001735, NIGP01001852, NIGP01002067, NIGP01000332, NIGP01000588, NIGP01001651, NIGP01001665, NIGP01001990, NIGP01000226, NIGP01000358, NIGP01000825, NIGP01000917, NIGP01000946, NIGP01001002, NIGP01001056, NIGP01001101, NIGP01001349, NIGP01001814, NIGP01002025, NIGP01001900
##   - in 'y': NIGP01000006, NIGP01000009, NIGP01000010, NIGP01000015, NIGP01000025, NIGP01000028, NIGP01000033, NIGP01000036, NIGP01000043, NIGP01000049, NIGP01000051, NIGP01000052, NIGP01000055, NIGP01000056, NIGP01000062, NIGP01000063, NIGP01000064, NIGP01000073, NIGP01000075, NIGP01000076, NIGP01000077, NIGP01000079, NIGP01000080, NIGP01000083, NIGP01000087, NIGP01000094, NIGP01000096, NIGP01000101, NIGP01000102, NIGP01000104, NIGP01000106, NIGP01000107, NIGP01000110, NIGP01000115, NIGP01000116, NIGP01000117, NIGP01000121, NIGP01000123, NIGP01000124, NIGP01000125, NIGP01000129, NIGP01000130, NIGP01000133, NIGP01000134, NIGP01000137, NIGP01000139, NIGP01000144, NIGP01000149, NIGP01000156, NIGP01000158, NIGP01000159, NIGP01000172, NIGP01000177, NIGP01000180, NIGP01000183, NIGP01000184, NIGP01000185, NIGP01000186, NIGP01000187, NIGP01000188, NIGP01000189, NIGP01000197, NIGP01000198, NIGP01000200, NIGP01000201, NIGP01000203, NIGP01000204, NIGP01000205, NIGP01000206, NIGP01000207, NIGP01000210, NIGP01000212, NIGP01000213, NIGP01000216, NIGP01000218, NIGP01000220, NIGP01000221, NIGP01000222, NIGP01000223, NIGP01000225, NIGP01000228, NIGP01000230, NIGP01000236, NIGP01000238, NIGP01000239, NIGP01000240, NIGP01000244, NIGP01000247, NIGP01000248, NIGP01000250, NIGP01000253, NIGP01000254, NIGP01000256, NIGP01000257, NIGP01000262, NIGP01000263, NIGP01000265, NIGP01000267, NIGP01000270, NIGP01000280, NIGP01000281, NIGP01000288, NIGP01000290, NIGP01000292, NIGP01000294, NIGP01000295, NIGP01000297, NIGP01000298, NIGP01000309, NIGP01000310, NIGP01000312, NIGP01000315, NIGP01000319, NIGP01000324, NIGP01000325, NIGP01000329, NIGP01000330, NIGP01000345, NIGP01000349, NIGP01000351, NIGP01000352, NIGP01000356, NIGP01000357, NIGP01000359, NIGP01000363, NIGP01000365, NIGP01000371, NIGP01000374, NIGP01000375, NIGP01000376, NIGP01000377, NIGP01000379, NIGP01000383, NIGP01000386, NIGP01000396, NIGP01000397, NIGP01000407, NIGP01000410, NIGP01000412, NIGP01000413, NIGP01000415, NIGP01000417, NIGP01000421, NIGP01000422, NIGP01000424, NIGP01000428, NIGP01000430, NIGP01000432, NIGP01000434, NIGP01000437, NIGP01000440, NIGP01000441, NIGP01000445, NIGP01000451, NIGP01000452, NIGP01000461, NIGP01000463, NIGP01000465, NIGP01000466, NIGP01000475, NIGP01000481, NIGP01000482, NIGP01000489, NIGP01000490, NIGP01000495, NIGP01000497, NIGP01000501, NIGP01000507, NIGP01000514, NIGP01000515, NIGP01000518, NIGP01000519, NIGP01000520, NIGP01000521, NIGP01000524, NIGP01000525, NIGP01000530, NIGP01000531, NIGP01000532, NIGP01000535, NIGP01000536, NIGP01000537, NIGP01000539, NIGP01000541, NIGP01000552, NIGP01000553, NIGP01000556, NIGP01000557, NIGP01000560, NIGP01000561, NIGP01000566, NIGP01000569, NIGP01000570, NIGP01000571, NIGP01000573, NIGP01000574, NIGP01000579, NIGP01000590, NIGP01000591, NIGP01000596, NIGP01000598, NIGP01000599, NIGP01000600, NIGP01000601, NIGP01000602, NIGP01000604, NIGP01000608, NIGP01000610, NIGP01000612, NIGP01000622, NIGP01000627, NIGP01000630, NIGP01000633, NIGP01000634, NIGP01000635, NIGP01000639, NIGP01000640, NIGP01000648, NIGP01000649, NIGP01000650, NIGP01000651, NIGP01000657, NIGP01000658, NIGP01000660, NIGP01000662, NIGP01000665, NIGP01000666, NIGP01000667, NIGP01000669, NIGP01000673, NIGP01000676, NIGP01000681, NIGP01000684, NIGP01000686, NIGP01000687, NIGP01000690, NIGP01000692, NIGP01000695, NIGP01000699, NIGP01000702, NIGP01000703, NIGP01000706, NIGP01000709, NIGP01000710, NIGP01000712, NIGP01000714, NIGP01000715, NIGP01000716, NIGP01000718, NIGP01000721, NIGP01000724, NIGP01000727, NIGP01000730, NIGP01000734, NIGP01000737, NIGP01000740, NIGP01000745, NIGP01000751, NIGP01000754, NIGP01000756, NIGP01000760, NIGP01000761, NIGP01000775, NIGP01000778, NIGP01000779, NIGP01000781, NIGP01000782, NIGP01000783, NIGP01000791, NIGP01000799, NIGP01000802, NIGP01000806, NIGP01000807, NIGP01000811, NIGP01000812, NIGP01000813, NIGP01000818, NIGP01000821, NIGP01000822, NIGP01000823, NIGP01000826, NIGP01000827, NIGP01000835, NIGP01000843, NIGP01000846, NIGP01000847, NIGP01000848, NIGP01000849, NIGP01000850, NIGP01000856, NIGP01000859, NIGP01000860, NIGP01000861, NIGP01000867, NIGP01000870, NIGP01000882, NIGP01000883, NIGP01000885, NIGP01000892, NIGP01000896, NIGP01000900, NIGP01000904, NIGP01000905, NIGP01000906, NIGP01000910, NIGP01000915, NIGP01000920, NIGP01000921, NIGP01000923, NIGP01000929, NIGP01000932, NIGP01000937, NIGP01000938, NIGP01000939, NIGP01000941, NIGP01000942, NIGP01000944, NIGP01000947, NIGP01000948, NIGP01000952, NIGP01000954, NIGP01000957, NIGP01000958, NIGP01000959, NIGP01000960, NIGP01000976, NIGP01000977, NIGP01000978, NIGP01000980, NIGP01000983, NIGP01000986, NIGP01000991, NIGP01000996, NIGP01001003, NIGP01001006, NIGP01001008, NIGP01001010, NIGP01001013, NIGP01001015, NIGP01001018, NIGP01001022, NIGP01001023, NIGP01001024, NIGP01001031, NIGP01001032, NIGP01001035, NIGP01001039, NIGP01001041, NIGP01001043, NIGP01001046, NIGP01001047, NIGP01001053, NIGP01001055, NIGP01001057, NIGP01001059, NIGP01001061, NIGP01001068, NIGP01001070, NIGP01001072, NIGP01001074, NIGP01001075, NIGP01001081, NIGP01001082, NIGP01001083, NIGP01001085, NIGP01001086, NIGP01001092, NIGP01001097, NIGP01001100, NIGP01001102, NIGP01001108, NIGP01001110, NIGP01001119, NIGP01001126, NIGP01001136, NIGP01001165, NIGP01001173, NIGP01001180, NIGP01001185, NIGP01001186, NIGP01001196, NIGP01001197, NIGP01001208, NIGP01001211, NIGP01001214, NIGP01001216, NIGP01001230, NIGP01001233, NIGP01001237, NIGP01001238, NIGP01001240, NIGP01001243, NIGP01001247, NIGP01001249, NIGP01001254, NIGP01001255, NIGP01001256, NIGP01001262, NIGP01001263, NIGP01001282, NIGP01001285, NIGP01001287, NIGP01001295, NIGP01001296, NIGP01001297, NIGP01001301, NIGP01001311, NIGP01001322, NIGP01001325, NIGP01001329, NIGP01001335, NIGP01001341, NIGP01001343, NIGP01001348, NIGP01001350, NIGP01001352, NIGP01001353, NIGP01001355, NIGP01001363, NIGP01001365, NIGP01001372, NIGP01001373, NIGP01001374, NIGP01001377, NIGP01001382, NIGP01001386, NIGP01001397, NIGP01001398, NIGP01001407, NIGP01001408, NIGP01001414, NIGP01001415, NIGP01001416, NIGP01001417, NIGP01001426, NIGP01001431, NIGP01001438, NIGP01001442, NIGP01001450, NIGP01001455, NIGP01001458, NIGP01001463, NIGP01001464, NIGP01001468, NIGP01001469, NIGP01001476, NIGP01001477, NIGP01001478, NIGP01001480, NIGP01001482, NIGP01001497, NIGP01001501, NIGP01001506, NIGP01001507, NIGP01001509, NIGP01001516, NIGP01001519, NIGP01001520, NIGP01001522, NIGP01001530, NIGP01001531, NIGP01001534, NIGP01001536, NIGP01001546, NIGP01001547, NIGP01001549, NIGP01001551, NIGP01001553, NIGP01001557, NIGP01001562, NIGP01001568, NIGP01001572, NIGP01001573, NIGP01001574, NIGP01001575, NIGP01001576, NIGP01001578, NIGP01001580, NIGP01001587, NIGP01001589, NIGP01001591, NIGP01001593, NIGP01001597, NIGP01001599, NIGP01001603, NIGP01001614, NIGP01001615, NIGP01001617, NIGP01001618, NIGP01001622, NIGP01001624, NIGP01001630, NIGP01001639, NIGP01001640, NIGP01001641, NIGP01001645, NIGP01001646, NIGP01001648, NIGP01001661, NIGP01001671, NIGP01001672, NIGP01001675, NIGP01001676, NIGP01001678, NIGP01001682, NIGP01001690, NIGP01001692, NIGP01001696, NIGP01001699, NIGP01001702, NIGP01001703, NIGP01001705, NIGP01001706, NIGP01001711, NIGP01001712, NIGP01001713, NIGP01001717, NIGP01001719, NIGP01001726, NIGP01001727, NIGP01001728, NIGP01001729, NIGP01001730, NIGP01001732, NIGP01001736, NIGP01001738, NIGP01001743, NIGP01001749, NIGP01001750, NIGP01001752, NIGP01001755, NIGP01001756, NIGP01001758, NIGP01001766, NIGP01001767, NIGP01001769, NIGP01001770, NIGP01001774, NIGP01001784, NIGP01001786, NIGP01001788, NIGP01001789, NIGP01001800, NIGP01001801, NIGP01001810, NIGP01001811, NIGP01001816, NIGP01001817, NIGP01001818, NIGP01001819, NIGP01

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': NIGP01000081, NIGP01000723, NIGP01001312, NIGP01001552, NIGP01001579, NIGP01001581, NIGP01001642, NIGP01001658, NIGP01001735, NIGP01001852, NIGP01002067, NIGP01000332, NIGP01000588, NIGP01001651, NIGP01001665, NIGP01001990, NIGP01000226, NIGP01000358, NIGP01000825, NIGP01000917, NIGP01000946, NIGP01001002, NIGP01001056, NIGP01001101, NIGP01001349, NIGP01001814, NIGP01002025, NIGP01001900
##   - in 'y': NIGP01000006, NIGP01000009, NIGP01000010, NIGP01000015, NIGP01000025, NIGP01000028, NIGP01000033, NIGP01000036, NIGP01000043, NIGP01000049, NIGP01000051, NIGP01000052, NIGP01000055, NIGP01000056, NIGP01000062, NIGP01000063, NIGP01000064, NIGP01000073, NIGP01000075, NIGP01000076, NIGP01000077, NIGP01000079, NIGP01000080, NIGP01000083, NIGP01000087, NIGP01000094, NIGP01000096, NIGP01000101, NIGP01000102, NIGP01000104, NIGP01000106, NIGP01000107, NIGP01000110, NIGP01000115, NIGP01000116, NIGP01000117, NIGP01000121, NIGP01000123, NIGP01000124, NIGP01000125, NIGP01000129, NIGP01000130, NIGP01000133, NIGP01000134, NIGP01000137, NIGP01000139, NIGP01000144, NIGP01000149, NIGP01000156, NIGP01000158, NIGP01000159, NIGP01000172, NIGP01000177, NIGP01000180, NIGP01000183, NIGP01000184, NIGP01000185, NIGP01000186, NIGP01000187, NIGP01000188, NIGP01000189, NIGP01000197, NIGP01000198, NIGP01000200, NIGP01000201, NIGP01000203, NIGP01000204, NIGP01000205, NIGP01000206, NIGP01000207, NIGP01000210, NIGP01000212, NIGP01000213, NIGP01000216, NIGP01000218, NIGP01000220, NIGP01000221, NIGP01000222, NIGP01000223, NIGP01000225, NIGP01000228, NIGP01000230, NIGP01000236, NIGP01000238, NIGP01000239, NIGP01000240, NIGP01000244, NIGP01000247, NIGP01000248, NIGP01000250, NIGP01000253, NIGP01000254, NIGP01000256, NIGP01000257, NIGP01000262, NIGP01000263, NIGP01000265, NIGP01000267, NIGP01000270, NIGP01000280, NIGP01000281, NIGP01000288, NIGP01000290, NIGP01000292, NIGP01000294, NIGP01000295, NIGP01000297, NIGP01000298, NIGP01000309, NIGP01000310, NIGP01000312, NIGP01000315, NIGP01000319, NIGP01000324, NIGP01000325, NIGP01000329, NIGP01000330, NIGP01000345, NIGP01000349, NIGP01000351, NIGP01000352, NIGP01000356, NIGP01000357, NIGP01000359, NIGP01000363, NIGP01000365, NIGP01000371, NIGP01000374, NIGP01000375, NIGP01000376, NIGP01000377, NIGP01000379, NIGP01000383, NIGP01000386, NIGP01000396, NIGP01000397, NIGP01000407, NIGP01000410, NIGP01000412, NIGP01000413, NIGP01000415, NIGP01000417, NIGP01000421, NIGP01000422, NIGP01000424, NIGP01000428, NIGP01000430, NIGP01000432, NIGP01000434, NIGP01000437, NIGP01000440, NIGP01000441, NIGP01000445, NIGP01000451, NIGP01000452, NIGP01000461, NIGP01000463, NIGP01000465, NIGP01000466, NIGP01000475, NIGP01000481, NIGP01000482, NIGP01000489, NIGP01000490, NIGP01000495, NIGP01000497, NIGP01000501, NIGP01000507, NIGP01000514, NIGP01000515, NIGP01000518, NIGP01000519, NIGP01000520, NIGP01000521, NIGP01000524, NIGP01000525, NIGP01000530, NIGP01000531, NIGP01000532, NIGP01000535, NIGP01000536, NIGP01000537, NIGP01000539, NIGP01000541, NIGP01000552, NIGP01000553, NIGP01000556, NIGP01000557, NIGP01000560, NIGP01000561, NIGP01000566, NIGP01000569, NIGP01000570, NIGP01000571, NIGP01000573, NIGP01000574, NIGP01000579, NIGP01000590, NIGP01000591, NIGP01000596, NIGP01000598, NIGP01000599, NIGP01000600, NIGP01000601, NIGP01000602, NIGP01000604, NIGP01000608, NIGP01000610, NIGP01000612, NIGP01000622, NIGP01000627, NIGP01000630, NIGP01000633, NIGP01000634, NIGP01000635, NIGP01000639, NIGP01000640, NIGP01000648, NIGP01000649, NIGP01000650, NIGP01000651, NIGP01000657, NIGP01000658, NIGP01000660, NIGP01000662, NIGP01000665, NIGP01000666, NIGP01000667, NIGP01000669, NIGP01000673, NIGP01000676, NIGP01000681, NIGP01000684, NIGP01000686, NIGP01000687, NIGP01000690, NIGP01000692, NIGP01000695, NIGP01000699, NIGP01000702, NIGP01000703, NIGP01000706, NIGP01000709, NIGP01000710, NIGP01000712, NIGP01000714, NIGP01000715, NIGP01000716, NIGP01000718, NIGP01000721, NIGP01000724, NIGP01000727, NIGP01000730, NIGP01000734, NIGP01000737, NIGP01000740, NIGP01000745, NIGP01000751, NIGP01000754, NIGP01000756, NIGP01000760, NIGP01000761, NIGP01000775, NIGP01000778, NIGP01000779, NIGP01000781, NIGP01000782, NIGP01000783, NIGP01000791, NIGP01000799, NIGP01000802, NIGP01000806, NIGP01000807, NIGP01000811, NIGP01000812, NIGP01000813, NIGP01000818, NIGP01000821, NIGP01000822, NIGP01000823, NIGP01000826, NIGP01000827, NIGP01000835, NIGP01000843, NIGP01000846, NIGP01000847, NIGP01000848, NIGP01000849, NIGP01000850, NIGP01000856, NIGP01000859, NIGP01000860, NIGP01000861, NIGP01000867, NIGP01000870, NIGP01000882, NIGP01000883, NIGP01000885, NIGP01000892, NIGP01000896, NIGP01000900, NIGP01000904, NIGP01000905, NIGP01000906, NIGP01000910, NIGP01000915, NIGP01000920, NIGP01000921, NIGP01000923, NIGP01000929, NIGP01000932, NIGP01000937, NIGP01000938, NIGP01000939, NIGP01000941, NIGP01000942, NIGP01000944, NIGP01000947, NIGP01000948, NIGP01000952, NIGP01000954, NIGP01000957, NIGP01000958, NIGP01000959, NIGP01000960, NIGP01000976, NIGP01000977, NIGP01000978, NIGP01000980, NIGP01000983, NIGP01000986, NIGP01000991, NIGP01000996, NIGP01001003, NIGP01001006, NIGP01001008, NIGP01001010, NIGP01001013, NIGP01001015, NIGP01001018, NIGP01001022, NIGP01001023, NIGP01001024, NIGP01001031, NIGP01001032, NIGP01001035, NIGP01001039, NIGP01001041, NIGP01001043, NIGP01001046, NIGP01001047, NIGP01001053, NIGP01001055, NIGP01001057, NIGP01001059, NIGP01001061, NIGP01001068, NIGP01001070, NIGP01001072, NIGP01001074, NIGP01001075, NIGP01001081, NIGP01001082, NIGP01001083, NIGP01001085, NIGP01001086, NIGP01001092, NIGP01001097, NIGP01001100, NIGP01001102, NIGP01001108, NIGP01001110, NIGP01001119, NIGP01001126, NIGP01001136, NIGP01001165, NIGP01001173, NIGP01001180, NIGP01001185, NIGP01001186, NIGP01001196, NIGP01001197, NIGP01001208, NIGP01001211, NIGP01001214, NIGP01001216, NIGP01001230, NIGP01001233, NIGP01001237, NIGP01001238, NIGP01001240, NIGP01001243, NIGP01001247, NIGP01001249, NIGP01001254, NIGP01001255, NIGP01001256, NIGP01001262, NIGP01001263, NIGP01001282, NIGP01001285, NIGP01001287, NIGP01001295, NIGP01001296, NIGP01001297, NIGP01001301, NIGP01001311, NIGP01001322, NIGP01001325, NIGP01001329, NIGP01001335, NIGP01001341, NIGP01001343, NIGP01001348, NIGP01001350, NIGP01001352, NIGP01001353, NIGP01001355, NIGP01001363, NIGP01001365, NIGP01001372, NIGP01001373, NIGP01001374, NIGP01001377, NIGP01001382, NIGP01001386, NIGP01001397, NIGP01001398, NIGP01001407, NIGP01001408, NIGP01001414, NIGP01001415, NIGP01001416, NIGP01001417, NIGP01001426, NIGP01001431, NIGP01001438, NIGP01001442, NIGP01001450, NIGP01001455, NIGP01001458, NIGP01001463, NIGP01001464, NIGP01001468, NIGP01001469, NIGP01001476, NIGP01001477, NIGP01001478, NIGP01001480, NIGP01001482, NIGP01001497, NIGP01001501, NIGP01001506, NIGP01001507, NIGP01001509, NIGP01001516, NIGP01001519, NIGP01001520, NIGP01001522, NIGP01001530, NIGP01001531, NIGP01001534, NIGP01001536, NIGP01001546, NIGP01001547, NIGP01001549, NIGP01001551, NIGP01001553, NIGP01001557, NIGP01001562, NIGP01001568, NIGP01001572, NIGP01001573, NIGP01001574, NIGP01001575, NIGP01001576, NIGP01001578, NIGP01001580, NIGP01001587, NIGP01001589, NIGP01001591, NIGP01001593, NIGP01001597, NIGP01001599, NIGP01001603, NIGP01001614, NIGP01001615, NIGP01001617, NIGP01001618, NIGP01001622, NIGP01001624, NIGP01001630, NIGP01001639, NIGP01001640, NIGP01001641, NIGP01001645, NIGP01001646, NIGP01001648, NIGP01001661, NIGP01001671, NIGP01001672, NIGP01001675, NIGP01001676, NIGP01001678, NIGP01001682, NIGP01001690, NIGP01001692, NIGP01001696, NIGP01001699, NIGP01001702, NIGP01001703, NIGP01001705, NIGP01001706, NIGP01001711, NIGP01001712, NIGP01001713, NIGP01001717, NIGP01001719, NIGP01001726, NIGP01001727, NIGP01001728, NIGP01001729, NIGP01001730, NIGP01001732, NIGP01001736, NIGP01001738, NIGP01001743, NIGP01001749, NIGP01001750, NIGP01001752, NIGP01001755, NIGP01001756, NIGP01001758, NIGP01001766, NIGP01001767, NIGP01001769, NIGP01001770, NIGP01001774, NIGP01001784, NIGP01001786, NIGP01001788, NIGP01001789, NIGP01001800, NIGP01001801, NIGP01001810, NIGP01001811, NIGP01001816, NIGP01001817, NIGP01001818, NIGP01001819, NIGP01

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': NIGP01000081, NIGP01000723, NIGP01001312, NIGP01001552, NIGP01001579, NIGP01001581, NIGP01001642, NIGP01001658, NIGP01001735, NIGP01001852, NIGP01002067, NIGP01000332, NIGP01000588, NIGP01001651, NIGP01001665, NIGP01001990, NIGP01000226, NIGP01000358, NIGP01000825, NIGP01000917, NIGP01000946, NIGP01001002, NIGP01001056, NIGP01001101, NIGP01001349, NIGP01001814, NIGP01002025, NIGP01001900
##   - in 'y': NIGP01000006, NIGP01000009, NIGP01000010, NIGP01000015, NIGP01000025, NIGP01000028, NIGP01000033, NIGP01000036, NIGP01000043, NIGP01000049, NIGP01000051, NIGP01000052, NIGP01000055, NIGP01000056, NIGP01000062, NIGP01000063, NIGP01000064, NIGP01000073, NIGP01000075, NIGP01000076, NIGP01000077, NIGP01000079, NIGP01000080, NIGP01000083, NIGP01000087, NIGP01000094, NIGP01000096, NIGP01000101, NIGP01000102, NIGP01000104, NIGP01000106, NIGP01000107, NIGP01000110, NIGP01000115, NIGP01000116, NIGP01000117, NIGP01000121, NIGP01000123, NIGP01000124, NIGP01000125, NIGP01000129, NIGP01000130, NIGP01000133, NIGP01000134, NIGP01000137, NIGP01000139, NIGP01000144, NIGP01000149, NIGP01000156, NIGP01000158, NIGP01000159, NIGP01000172, NIGP01000177, NIGP01000180, NIGP01000183, NIGP01000184, NIGP01000185, NIGP01000186, NIGP01000187, NIGP01000188, NIGP01000189, NIGP01000197, NIGP01000198, NIGP01000200, NIGP01000201, NIGP01000203, NIGP01000204, NIGP01000205, NIGP01000206, NIGP01000207, NIGP01000210, NIGP01000212, NIGP01000213, NIGP01000216, NIGP01000218, NIGP01000220, NIGP01000221, NIGP01000222, NIGP01000223, NIGP01000225, NIGP01000228, NIGP01000230, NIGP01000236, NIGP01000238, NIGP01000239, NIGP01000240, NIGP01000244, NIGP01000247, NIGP01000248, NIGP01000250, NIGP01000253, NIGP01000254, NIGP01000256, NIGP01000257, NIGP01000262, NIGP01000263, NIGP01000265, NIGP01000267, NIGP01000270, NIGP01000280, NIGP01000281, NIGP01000288, NIGP01000290, NIGP01000292, NIGP01000294, NIGP01000295, NIGP01000297, NIGP01000298, NIGP01000309, NIGP01000310, NIGP01000312, NIGP01000315, NIGP01000319, NIGP01000324, NIGP01000325, NIGP01000329, NIGP01000330, NIGP01000345, NIGP01000349, NIGP01000351, NIGP01000352, NIGP01000356, NIGP01000357, NIGP01000359, NIGP01000363, NIGP01000365, NIGP01000371, NIGP01000374, NIGP01000375, NIGP01000376, NIGP01000377, NIGP01000379, NIGP01000383, NIGP01000386, NIGP01000396, NIGP01000397, NIGP01000407, NIGP01000410, NIGP01000412, NIGP01000413, NIGP01000415, NIGP01000417, NIGP01000421, NIGP01000422, NIGP01000424, NIGP01000428, NIGP01000430, NIGP01000432, NIGP01000434, NIGP01000437, NIGP01000440, NIGP01000441, NIGP01000445, NIGP01000451, NIGP01000452, NIGP01000461, NIGP01000463, NIGP01000465, NIGP01000466, NIGP01000475, NIGP01000481, NIGP01000482, NIGP01000489, NIGP01000490, NIGP01000495, NIGP01000497, NIGP01000501, NIGP01000507, NIGP01000514, NIGP01000515, NIGP01000518, NIGP01000519, NIGP01000520, NIGP01000521, NIGP01000524, NIGP01000525, NIGP01000530, NIGP01000531, NIGP01000532, NIGP01000535, NIGP01000536, NIGP01000537, NIGP01000539, NIGP01000541, NIGP01000552, NIGP01000553, NIGP01000556, NIGP01000557, NIGP01000560, NIGP01000561, NIGP01000566, NIGP01000569, NIGP01000570, NIGP01000571, NIGP01000573, NIGP01000574, NIGP01000579, NIGP01000590, NIGP01000591, NIGP01000596, NIGP01000598, NIGP01000599, NIGP01000600, NIGP01000601, NIGP01000602, NIGP01000604, NIGP01000608, NIGP01000610, NIGP01000612, NIGP01000622, NIGP01000627, NIGP01000630, NIGP01000633, NIGP01000634, NIGP01000635, NIGP01000639, NIGP01000640, NIGP01000648, NIGP01000649, NIGP01000650, NIGP01000651, NIGP01000657, NIGP01000658, NIGP01000660, NIGP01000662, NIGP01000665, NIGP01000666, NIGP01000667, NIGP01000669, NIGP01000673, NIGP01000676, NIGP01000681, NIGP01000684, NIGP01000686, NIGP01000687, NIGP01000690, NIGP01000692, NIGP01000695, NIGP01000699, NIGP01000702, NIGP01000703, NIGP01000706, NIGP01000709, NIGP01000710, NIGP01000712, NIGP01000714, NIGP01000715, NIGP01000716, NIGP01000718, NIGP01000721, NIGP01000724, NIGP01000727, NIGP01000730, NIGP01000734, NIGP01000737, NIGP01000740, NIGP01000745, NIGP01000751, NIGP01000754, NIGP01000756, NIGP01000760, NIGP01000761, NIGP01000775, NIGP01000778, NIGP01000779, NIGP01000781, NIGP01000782, NIGP01000783, NIGP01000791, NIGP01000799, NIGP01000802, NIGP01000806, NIGP01000807, NIGP01000811, NIGP01000812, NIGP01000813, NIGP01000818, NIGP01000821, NIGP01000822, NIGP01000823, NIGP01000826, NIGP01000827, NIGP01000835, NIGP01000843, NIGP01000846, NIGP01000847, NIGP01000848, NIGP01000849, NIGP01000850, NIGP01000856, NIGP01000859, NIGP01000860, NIGP01000861, NIGP01000867, NIGP01000870, NIGP01000882, NIGP01000883, NIGP01000885, NIGP01000892, NIGP01000896, NIGP01000900, NIGP01000904, NIGP01000905, NIGP01000906, NIGP01000910, NIGP01000915, NIGP01000920, NIGP01000921, NIGP01000923, NIGP01000929, NIGP01000932, NIGP01000937, NIGP01000938, NIGP01000939, NIGP01000941, NIGP01000942, NIGP01000944, NIGP01000947, NIGP01000948, NIGP01000952, NIGP01000954, NIGP01000957, NIGP01000958, NIGP01000959, NIGP01000960, NIGP01000976, NIGP01000977, NIGP01000978, NIGP01000980, NIGP01000983, NIGP01000986, NIGP01000991, NIGP01000996, NIGP01001003, NIGP01001006, NIGP01001008, NIGP01001010, NIGP01001013, NIGP01001015, NIGP01001018, NIGP01001022, NIGP01001023, NIGP01001024, NIGP01001031, NIGP01001032, NIGP01001035, NIGP01001039, NIGP01001041, NIGP01001043, NIGP01001046, NIGP01001047, NIGP01001053, NIGP01001055, NIGP01001057, NIGP01001059, NIGP01001061, NIGP01001068, NIGP01001070, NIGP01001072, NIGP01001074, NIGP01001075, NIGP01001081, NIGP01001082, NIGP01001083, NIGP01001085, NIGP01001086, NIGP01001092, NIGP01001097, NIGP01001100, NIGP01001102, NIGP01001108, NIGP01001110, NIGP01001119, NIGP01001126, NIGP01001136, NIGP01001165, NIGP01001173, NIGP01001180, NIGP01001185, NIGP01001186, NIGP01001196, NIGP01001197, NIGP01001208, NIGP01001211, NIGP01001214, NIGP01001216, NIGP01001230, NIGP01001233, NIGP01001237, NIGP01001238, NIGP01001240, NIGP01001243, NIGP01001247, NIGP01001249, NIGP01001254, NIGP01001255, NIGP01001256, NIGP01001262, NIGP01001263, NIGP01001282, NIGP01001285, NIGP01001287, NIGP01001295, NIGP01001296, NIGP01001297, NIGP01001301, NIGP01001311, NIGP01001322, NIGP01001325, NIGP01001329, NIGP01001335, NIGP01001341, NIGP01001343, NIGP01001348, NIGP01001350, NIGP01001352, NIGP01001353, NIGP01001355, NIGP01001363, NIGP01001365, NIGP01001372, NIGP01001373, NIGP01001374, NIGP01001377, NIGP01001382, NIGP01001386, NIGP01001397, NIGP01001398, NIGP01001407, NIGP01001408, NIGP01001414, NIGP01001415, NIGP01001416, NIGP01001417, NIGP01001426, NIGP01001431, NIGP01001438, NIGP01001442, NIGP01001450, NIGP01001455, NIGP01001458, NIGP01001463, NIGP01001464, NIGP01001468, NIGP01001469, NIGP01001476, NIGP01001477, NIGP01001478, NIGP01001480, NIGP01001482, NIGP01001497, NIGP01001501, NIGP01001506, NIGP01001507, NIGP01001509, NIGP01001516, NIGP01001519, NIGP01001520, NIGP01001522, NIGP01001530, NIGP01001531, NIGP01001534, NIGP01001536, NIGP01001546, NIGP01001547, NIGP01001549, NIGP01001551, NIGP01001553, NIGP01001557, NIGP01001562, NIGP01001568, NIGP01001572, NIGP01001573, NIGP01001574, NIGP01001575, NIGP01001576, NIGP01001578, NIGP01001580, NIGP01001587, NIGP01001589, NIGP01001591, NIGP01001593, NIGP01001597, NIGP01001599, NIGP01001603, NIGP01001614, NIGP01001615, NIGP01001617, NIGP01001618, NIGP01001622, NIGP01001624, NIGP01001630, NIGP01001639, NIGP01001640, NIGP01001641, NIGP01001645, NIGP01001646, NIGP01001648, NIGP01001661, NIGP01001671, NIGP01001672, NIGP01001675, NIGP01001676, NIGP01001678, NIGP01001682, NIGP01001690, NIGP01001692, NIGP01001696, NIGP01001699, NIGP01001702, NIGP01001703, NIGP01001705, NIGP01001706, NIGP01001711, NIGP01001712, NIGP01001713, NIGP01001717, NIGP01001719, NIGP01001726, NIGP01001727, NIGP01001728, NIGP01001729, NIGP01001730, NIGP01001732, NIGP01001736, NIGP01001738, NIGP01001743, NIGP01001749, NIGP01001750, NIGP01001752, NIGP01001755, NIGP01001756, NIGP01001758, NIGP01001766, NIGP01001767, NIGP01001769, NIGP01001770, NIGP01001774, NIGP01001784, NIGP01001786, NIGP01001788, NIGP01001789, NIGP01001800, NIGP01001801, NIGP01001810, NIGP01001811, NIGP01001816, NIGP01001817, NIGP01001818, NIGP01001819, NIGP01

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': NIGP01000081, NIGP01000723, NIGP01001312, NIGP01001552, NIGP01001579, NIGP01001581, NIGP01001642, NIGP01001658, NIGP01001735, NIGP01001852, NIGP01002067, NIGP01000332, NIGP01000588, NIGP01001651, NIGP01001665, NIGP01001990, NIGP01000226, NIGP01000358, NIGP01000825, NIGP01000917, NIGP01000946, NIGP01001002, NIGP01001056, NIGP01001101, NIGP01001349, NIGP01001814, NIGP01002025, NIGP01001900
##   - in 'y': NIGP01000006, NIGP01000009, NIGP01000010, NIGP01000015, NIGP01000025, NIGP01000028, NIGP01000033, NIGP01000036, NIGP01000043, NIGP01000049, NIGP01000051, NIGP01000052, NIGP01000055, NIGP01000056, NIGP01000062, NIGP01000063, NIGP01000064, NIGP01000073, NIGP01000075, NIGP01000076, NIGP01000077, NIGP01000079, NIGP01000080, NIGP01000083, NIGP01000087, NIGP01000094, NIGP01000096, NIGP01000101, NIGP01000102, NIGP01000104, NIGP01000106, NIGP01000107, NIGP01000110, NIGP01000115, NIGP01000116, NIGP01000117, NIGP01000121, NIGP01000123, NIGP01000124, NIGP01000125, NIGP01000129, NIGP01000130, NIGP01000133, NIGP01000134, NIGP01000137, NIGP01000139, NIGP01000144, NIGP01000149, NIGP01000156, NIGP01000158, NIGP01000159, NIGP01000172, NIGP01000177, NIGP01000180, NIGP01000183, NIGP01000184, NIGP01000185, NIGP01000186, NIGP01000187, NIGP01000188, NIGP01000189, NIGP01000197, NIGP01000198, NIGP01000200, NIGP01000201, NIGP01000203, NIGP01000204, NIGP01000205, NIGP01000206, NIGP01000207, NIGP01000210, NIGP01000212, NIGP01000213, NIGP01000216, NIGP01000218, NIGP01000220, NIGP01000221, NIGP01000222, NIGP01000223, NIGP01000225, NIGP01000228, NIGP01000230, NIGP01000236, NIGP01000238, NIGP01000239, NIGP01000240, NIGP01000244, NIGP01000247, NIGP01000248, NIGP01000250, NIGP01000253, NIGP01000254, NIGP01000256, NIGP01000257, NIGP01000262, NIGP01000263, NIGP01000265, NIGP01000267, NIGP01000270, NIGP01000280, NIGP01000281, NIGP01000288, NIGP01000290, NIGP01000292, NIGP01000294, NIGP01000295, NIGP01000297, NIGP01000298, NIGP01000309, NIGP01000310, NIGP01000312, NIGP01000315, NIGP01000319, NIGP01000324, NIGP01000325, NIGP01000329, NIGP01000330, NIGP01000345, NIGP01000349, NIGP01000351, NIGP01000352, NIGP01000356, NIGP01000357, NIGP01000359, NIGP01000363, NIGP01000365, NIGP01000371, NIGP01000374, NIGP01000375, NIGP01000376, NIGP01000377, NIGP01000379, NIGP01000383, NIGP01000386, NIGP01000396, NIGP01000397, NIGP01000407, NIGP01000410, NIGP01000412, NIGP01000413, NIGP01000415, NIGP01000417, NIGP01000421, NIGP01000422, NIGP01000424, NIGP01000428, NIGP01000430, NIGP01000432, NIGP01000434, NIGP01000437, NIGP01000440, NIGP01000441, NIGP01000445, NIGP01000451, NIGP01000452, NIGP01000461, NIGP01000463, NIGP01000465, NIGP01000466, NIGP01000475, NIGP01000481, NIGP01000482, NIGP01000489, NIGP01000490, NIGP01000495, NIGP01000497, NIGP01000501, NIGP01000507, NIGP01000514, NIGP01000515, NIGP01000518, NIGP01000519, NIGP01000520, NIGP01000521, NIGP01000524, NIGP01000525, NIGP01000530, NIGP01000531, NIGP01000532, NIGP01000535, NIGP01000536, NIGP01000537, NIGP01000539, NIGP01000541, NIGP01000552, NIGP01000553, NIGP01000556, NIGP01000557, NIGP01000560, NIGP01000561, NIGP01000566, NIGP01000569, NIGP01000570, NIGP01000571, NIGP01000573, NIGP01000574, NIGP01000579, NIGP01000590, NIGP01000591, NIGP01000596, NIGP01000598, NIGP01000599, NIGP01000600, NIGP01000601, NIGP01000602, NIGP01000604, NIGP01000608, NIGP01000610, NIGP01000612, NIGP01000622, NIGP01000627, NIGP01000630, NIGP01000633, NIGP01000634, NIGP01000635, NIGP01000639, NIGP01000640, NIGP01000648, NIGP01000649, NIGP01000650, NIGP01000651, NIGP01000657, NIGP01000658, NIGP01000660, NIGP01000662, NIGP01000665, NIGP01000666, NIGP01000667, NIGP01000669, NIGP01000673, NIGP01000676, NIGP01000681, NIGP01000684, NIGP01000686, NIGP01000687, NIGP01000690, NIGP01000692, NIGP01000695, NIGP01000699, NIGP01000702, NIGP01000703, NIGP01000706, NIGP01000709, NIGP01000710, NIGP01000712, NIGP01000714, NIGP01000715, NIGP01000716, NIGP01000718, NIGP01000721, NIGP01000724, NIGP01000727, NIGP01000730, NIGP01000734, NIGP01000737, NIGP01000740, NIGP01000745, NIGP01000751, NIGP01000754, NIGP01000756, NIGP01000760, NIGP01000761, NIGP01000775, NIGP01000778, NIGP01000779, NIGP01000781, NIGP01000782, NIGP01000783, NIGP01000791, NIGP01000799, NIGP01000802, NIGP01000806, NIGP01000807, NIGP01000811, NIGP01000812, NIGP01000813, NIGP01000818, NIGP01000821, NIGP01000822, NIGP01000823, NIGP01000826, NIGP01000827, NIGP01000835, NIGP01000843, NIGP01000846, NIGP01000847, NIGP01000848, NIGP01000849, NIGP01000850, NIGP01000856, NIGP01000859, NIGP01000860, NIGP01000861, NIGP01000867, NIGP01000870, NIGP01000882, NIGP01000883, NIGP01000885, NIGP01000892, NIGP01000896, NIGP01000900, NIGP01000904, NIGP01000905, NIGP01000906, NIGP01000910, NIGP01000915, NIGP01000920, NIGP01000921, NIGP01000923, NIGP01000929, NIGP01000932, NIGP01000937, NIGP01000938, NIGP01000939, NIGP01000941, NIGP01000942, NIGP01000944, NIGP01000947, NIGP01000948, NIGP01000952, NIGP01000954, NIGP01000957, NIGP01000958, NIGP01000959, NIGP01000960, NIGP01000976, NIGP01000977, NIGP01000978, NIGP01000980, NIGP01000983, NIGP01000986, NIGP01000991, NIGP01000996, NIGP01001003, NIGP01001006, NIGP01001008, NIGP01001010, NIGP01001013, NIGP01001015, NIGP01001018, NIGP01001022, NIGP01001023, NIGP01001024, NIGP01001031, NIGP01001032, NIGP01001035, NIGP01001039, NIGP01001041, NIGP01001043, NIGP01001046, NIGP01001047, NIGP01001053, NIGP01001055, NIGP01001057, NIGP01001059, NIGP01001061, NIGP01001068, NIGP01001070, NIGP01001072, NIGP01001074, NIGP01001075, NIGP01001081, NIGP01001082, NIGP01001083, NIGP01001085, NIGP01001086, NIGP01001092, NIGP01001097, NIGP01001100, NIGP01001102, NIGP01001108, NIGP01001110, NIGP01001119, NIGP01001126, NIGP01001136, NIGP01001165, NIGP01001173, NIGP01001180, NIGP01001185, NIGP01001186, NIGP01001196, NIGP01001197, NIGP01001208, NIGP01001211, NIGP01001214, NIGP01001216, NIGP01001230, NIGP01001233, NIGP01001237, NIGP01001238, NIGP01001240, NIGP01001243, NIGP01001247, NIGP01001249, NIGP01001254, NIGP01001255, NIGP01001256, NIGP01001262, NIGP01001263, NIGP01001282, NIGP01001285, NIGP01001287, NIGP01001295, NIGP01001296, NIGP01001297, NIGP01001301, NIGP01001311, NIGP01001322, NIGP01001325, NIGP01001329, NIGP01001335, NIGP01001341, NIGP01001343, NIGP01001348, NIGP01001350, NIGP01001352, NIGP01001353, NIGP01001355, NIGP01001363, NIGP01001365, NIGP01001372, NIGP01001373, NIGP01001374, NIGP01001377, NIGP01001382, NIGP01001386, NIGP01001397, NIGP01001398, NIGP01001407, NIGP01001408, NIGP01001414, NIGP01001415, NIGP01001416, NIGP01001417, NIGP01001426, NIGP01001431, NIGP01001438, NIGP01001442, NIGP01001450, NIGP01001455, NIGP01001458, NIGP01001463, NIGP01001464, NIGP01001468, NIGP01001469, NIGP01001476, NIGP01001477, NIGP01001478, NIGP01001480, NIGP01001482, NIGP01001497, NIGP01001501, NIGP01001506, NIGP01001507, NIGP01001509, NIGP01001516, NIGP01001519, NIGP01001520, NIGP01001522, NIGP01001530, NIGP01001531, NIGP01001534, NIGP01001536, NIGP01001546, NIGP01001547, NIGP01001549, NIGP01001551, NIGP01001553, NIGP01001557, NIGP01001562, NIGP01001568, NIGP01001572, NIGP01001573, NIGP01001574, NIGP01001575, NIGP01001576, NIGP01001578, NIGP01001580, NIGP01001587, NIGP01001589, NIGP01001591, NIGP01001593, NIGP01001597, NIGP01001599, NIGP01001603, NIGP01001614, NIGP01001615, NIGP01001617, NIGP01001618, NIGP01001622, NIGP01001624, NIGP01001630, NIGP01001639, NIGP01001640, NIGP01001641, NIGP01001645, NIGP01001646, NIGP01001648, NIGP01001661, NIGP01001671, NIGP01001672, NIGP01001675, NIGP01001676, NIGP01001678, NIGP01001682, NIGP01001690, NIGP01001692, NIGP01001696, NIGP01001699, NIGP01001702, NIGP01001703, NIGP01001705, NIGP01001706, NIGP01001711, NIGP01001712, NIGP01001713, NIGP01001717, NIGP01001719, NIGP01001726, NIGP01001727, NIGP01001728, NIGP01001729, NIGP01001730, NIGP01001732, NIGP01001736, NIGP01001738, NIGP01001743, NIGP01001749, NIGP01001750, NIGP01001752, NIGP01001755, NIGP01001756, NIGP01001758, NIGP01001766, NIGP01001767, NIGP01001769, NIGP01001770, NIGP01001774, NIGP01001784, NIGP01001786, NIGP01001788, NIGP01001789, NIGP01001800, NIGP01001801, NIGP01001810, NIGP01001811, NIGP01001816, NIGP01001817, NIGP01001818, NIGP01001819, NIGP01

## >> assigning chromosome lengths           2021-03-16 02:33:35 
## >> done...                    2021-03-16 02:33:35

plotAnnoPie(allanno)

kathrynrozengagnon/CLIPflexR documentation built on Dec. 8, 2022, 7:31 p.m.

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kathrynrozengagnon/CLIPflexR
CLIP tools and wrappers in R

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Process standard/BrdU-CLIP libraries using CLIPflexR

Initial processing and quality control

Decompress fastq files

You can look at the quality of your data (wrapping FASTX's quality stats)

Quality filter (wrapping FastX's quality filter)

Fastx_collapser (wrapping FASTX's fastx_collapser)

Follow these steps to process standard CLIP libraries

De-multiplex samples (wrapping FASTX's barcode splitter)

Now remove the 5' index, linker, and random barcode sequences (wrapping CTK's stripBarcode.pl)

Now remove the 3' linker (wrapping FASTX's clipper)

These reads are now ready to map to your genome

Follow these steps to process BrdU-CLIP libraries

First strip random barcode sequences (UMI) from the 5' end of reads (wrapping CTK's stripBarcode.pl)

De-multiplex samples (wrapping FASTX's barcode splitter)

Trim 3 "not G" (DDD) and index (6nt) from the 5' end of reads (wrapping FASTX's fastx_trimmer)

Fastx_clipper (wrapping FASTX's fastx_clipper)

Build a Bowtie2 genome index and align to genome using Rbowtie2.

Convert to beds, find peaks, and build count matrix

Convert to beds

Make tag directories and findpeaks (wrapping HOMER's MakeTagDirectory and findpeaks)

Make count matrix of peaks, starting with reading in HOMER peak files and making a matrix that indicated which peaks were called in each sample

The next step is to countFromBed to append the number of reads at each peak location, by sample

now you have your count matrix!

you can perform operations on sample groups to filter, visualize data, annotate your peaks, and more...

R Package Documentation

Browse R Packages

We want your feedback!

kathrynrozengagnon/CLIPflexR CLIP tools and wrappers in R

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Process standard/BrdU-CLIP libraries using CLIPflexR

Initial processing and quality control

Decompress fastq files

You can look at the quality of your data (wrapping FASTX's quality stats)

Quality filter (wrapping FastX's quality filter)

Fastx_collapser (wrapping FASTX's fastx_collapser)

Follow these steps to process standard CLIP libraries

De-multiplex samples (wrapping FASTX's barcode splitter)

Now remove the 5' index, linker, and random barcode sequences (wrapping CTK's stripBarcode.pl)

Now remove the 3' linker (wrapping FASTX's clipper)

These reads are now ready to map to your genome

Follow these steps to process BrdU-CLIP libraries

First strip random barcode sequences (UMI) from the 5' end of reads (wrapping CTK's stripBarcode.pl)

De-multiplex samples (wrapping FASTX's barcode splitter)

Trim 3 "not G" (DDD) and index (6nt) from the 5' end of reads (wrapping FASTX's fastx_trimmer)

Fastx_clipper (wrapping FASTX's fastx_clipper)

Build a Bowtie2 genome index and align to genome using Rbowtie2.

Convert to beds, find peaks, and build count matrix

Convert to beds

Make tag directories and findpeaks (wrapping HOMER's MakeTagDirectory and findpeaks)

Make count matrix of peaks, starting with reading in HOMER peak files and making a matrix that indicated which peaks were called in each sample

The next step is to countFromBed to append the number of reads at each peak location, by sample

now you have your count matrix!

you can perform operations on sample groups to filter, visualize data, annotate your peaks, and more...

R Package Documentation

Browse R Packages

We want your feedback!

kathrynrozengagnon/CLIPflexR
CLIP tools and wrappers in R