bowtie_align: Alignment using Rbowtie2
In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

bowtie_align

R Documentation

Alignment using Rbowtie2

Description

Alignment using Rbowtie2

Usage

bowtie_align(
  fq,
  index,
  outbam = "fq",
  inputFormat = "fasta",
  keepSAM = T,
  mode = "genome_map",
  maxMismatches = 0,
  seedSubString = 18,
  threads = 1,
  report_k = NULL,
  keep_all = NULL,
  soft_clip = NULL,
  additional_Args = NULL,
  overwrite = FALSE
)

Arguments

`fq`	path to file to process (fasta or fastq).
`index`	bowtie2 index name without extension.
`outbam`	output bam name, not required if mode is set. If mode is set to "NULL", specify "fq" (default - name of file to process/reads) or "index" (name of index)
`inputFormat`	Format of reads, "fastq" or "fasta" (default).
`keepSAM`	keep bowtie2 SAM output file, TRUE (default) or FALSE.
`mode`	mapping mode, "genome_map" (default - 1 mismatch in seed alignment, seed substring of 18) or "reverse_map" (for mapping short sequences to reads, i.e. miRNAs or chimera analysis, 0 mismatches and a seed substring of 18); set mode=NULL to custom set bowtie2 options using arguments below or additional arguments.
`maxMismatches`	max mismatches in seed alignment, (default is 0).
`seedSubString`	length of seed substrings (default is 18).
`threads`	number of threads to use (default is 1).
`report_k`	number of alignments to report, default is NULL (the best alignment is reported), set to integer to specify.
`keep_all`	report all alignments, default is NULL (the best alignment is reported), set to TRUE to report all.
`soft_clip`	allow soft clipping, default is NULL (no soft clipping), set to TRUE to to soft clip.
`additional_Args`	any additional mapping arguments not set above, default is NULL, can be set by specifying a single character string with spaces between arguments (see example below); run "Rbowtie2::bowtie2_usage()" to see all options; please note that due to a Rbowtie2 bug, the "–no-1mm-upfront" is not available.
`overwrite`	overwrite existing output files, TRUE or FALSE (default).

Value

path to sorted BAM.

Author(s)

Kathryn Rozen-Gagnon

Examples

testFasta <- system.file("extdata/hg19Small.fa",package="CLIPflexR")
myIndex <- suppressWarnings(bowtie2_index(testFasta, overwrite=TRUE))
testFQ <- system.file("extdata/Fox3_Std_small.fq.gz",package="CLIPflexR")
FqFile <- decompress(testFQ,overwrite=TRUE)
FqFile_FF <- ctk_fastqFilter(FqFile,qsFilter="mean:0-29:20",verbose=TRUE)
FqFile_clipped <- fastx_clipper(FqFile_FF,length=20)
FqFile_QF <- fastq_quality_trimmer(FqFile_clipped)
FqFile_Col <- ctk_fastq2collapse(FqFile_QF,verbose=TRUE)
FqFile_ColStrip <- ctk_stripBarcode(FqFile_Col,linkerlength=5, inputFormat="fastq")

##map reads to genome
suppressWarnings(bowtie_align(FqFile_ColStrip,myIndex,
inputFormat="fastq", overwrite=TRUE))

##map reads to genome, custom mode
suppressWarnings(bowtie_align(FqFile_ColStrip,myIndex, mode=NULL, 
soft_clip=TRUE, additional_Args="--mp 15 -R 4", inputFormat="fastq", overwrite=TRUE)) 

##map miRNAs to reads
miRNAs <- system.file("extdata/hsa_mature.fa",package="CLIPflexR")
FaFile_Fa <- fastx_qtoa(FqFile_ColStrip)
readIndex <- bowtie2_index(FaFile_Fa, overwrite=TRUE)
suppressWarnings(bowtie_align(miRNAs,readIndex, mode="reverse_map",overwrite=TRUE))

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