esATAC-package: An Easy-to-use Systematic pipeline for ATACseq data analysis

In esATAC: An Easy-to-use Systematic pipeline for ATACseq data analysis

Description

This package provides a framework and complete preset pipeline for the quantification and analysis of ATAC-seq Reads. It covers raw sequencing reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads file operation (SAM, BAM, and BED files), peak calling (fseq), genome annotations (Motif, GO, SNP analysis) and quality control report. The package is managed by dataflow graph. It is easy for user to pass variables seamlessly between processes and understand the workflow. Users can process FASTQ files through end-to-end preset pipeline which produces a pretty HTML report for quality control and preliminary statistical results, or customize workflow starting from any intermediate stages with esATAC functions easily and flexibly.

Preset pipeline for single replicate case study is shown below.

For multi-replicates case study, see atacRepsPipe.

For single replicate case-control study, see atacPipe2.

For multi-replicates case-control study, see atacRepsPipe2.

NOTE: Build bowtie index in the function may take some time. If you already have bowtie2 index files or you want to download(ftp://ftp.ccb.jhu.edu/pub/data/bowtie2_indexes) instead of building, you can let esATAC skip the steps by renaming them following the format (genome+suffix) and put them in reference installation path (refdir). Example: hg19 bowtie2 index files

• hg19.1.bt2

• hg19.2.bt2

• hg19.3.bt2

• hg19.4.bt2

• hg19.rev.1.bt2

• hg19.rev.2.bt2

For single end reads FASTQ files, The required parameters are fastqInput1 and adapter1. For paired end reads non-interleaved FASTQ files (interleave=FALSE,defualt), The required parameters are fastqInput1 and fastqInput2. Otherwise, parameter fastqInput2 is not required (interleave=TRUE)

The paths of sequencing data replicates can be a Character vector. For example:

fastqInput1=c("file_1.rep1.fastq","file_1.rep2.fastq")

fastqInput2=c("file_2.rep1.fastq","file_2.rep2.fastq")

The result will be return by the function. An HTML report file will be created for paired end reads. Intermediate files will be save at tmpdir path (default is ./)

Usage

atacPipe(
  genome,
  fastqInput1,
  fastqInput2 = NULL,
  tmpdir = file.path(getwd(), "esATAC-pipeline"),
  refdir = file.path(tmpdir, "refdir"),
  threads = 2,
  adapter1 = NULL,
  adapter2 = NULL,
  interleave = FALSE,
  basicAnalysis = FALSE,
  createReport = TRUE,
  motifs = NULL,
  pipelineName = "pipe",
  chr = c(1:22, "X", "Y"),
  p.cutoff = 1e-06,
  ...
)

Arguments

genome	Character scalar. The genome(like hg19, mm10, etc.) reference data in "refdir" to be used in the pipeline.
fastqInput1	Character vector. For single-end sequencing, it contains sequence file paths. For paired-end sequencing, it can be file paths with #1 mates paired with file paths in fastqInput2 And it can also be interleaved file paths when argument interleaved=TRUE
fastqInput2	Character vector. It contains file paths with #2 mates paired with file paths in fastqInput1. For single-end sequencing files and interleaved paired-end sequencing files(argument interleaved=TRUE), it must be NULL.
tmpdir	Character scalar. The temporary file storage path.
refdir	Character scalar. The path for reference data being installed to and storage.
threads	Integer scalar. The max threads allowed to be created.
adapter1	Character scalar. It is an adapter sequence for file1. For single end data, it is requied.
adapter2	Character scalar. It is an adapter sequence for file2.
interleave	Logical scalar. Set TRUE when files are interleaved paired-end sequencing data.
basicAnalysis	Logical scalar. If it is TRUE, the pipeline will skip the time consuming steps like GO annoation and motif analysis
createReport	Logical scalar. If the HTML report file will be created.
motifs	eitherPFMatrix, PFMatrixList, PWMatrix, PWMatrixList, default: vertebrates motif from JASPAR.
pipelineName	Character scalar. Temporary file prefix for identifying files when multiple pipeline generating file in the same tempdir.
chr	Which chromatin the program will processing. It must be identical with the filename of cut site information files or subset of . Default:c(1:22, "X", "Y").
p.cutoff	p-value cutoff for returning motifs, default: 1e-6.
...	Additional arguments, currently unused.

Details

See packageDescription('esATAC') for package details.

Value

List scalar. It is a list that save the result of the pipeline. Slot "filelist": the input file paths. Slot "wholesummary": a dataframe that for quality control summary Slot "atacProcs": ATACProc-class objects generated by each process in the pipeline. Slot "filtstat": a dataframe that summary the reads filted in each process.

Author(s)

Zheng Wei and Wei Zhang

See Also

printMap, atacPipe2, atacRenamer, atacRemoveAdapter, atacBowtie2Mapping, atacPeakCalling, atacMotifScan, atacRepsPipe, atacRepsPipe2

Examples

## Not run: 
## These codes are time consuming so they will not be run and
## checked by bioconductor checker.


# call pipeline
# for a quick example(only CTCF and BATF3 will be processing)
conclusion <-
  atacPipe(
       # MODIFY: Change these paths to your own case files!
       # e.g. fastqInput1 = "your/own/data/path.fastq"
       fastqInput1 = system.file(package="esATAC", "extdata", "chr20_1.1.fq.gz"),
       fastqInput2 = system.file(package="esATAC", "extdata", "chr20_2.1.fq.gz"),
       # MODIFY: Set the genome for your data
       genome = "hg19",
       motifs = getMotifInfo(motif.file = system.file("extdata", "CustomizedMotif.txt", package="esATAC")))

# call pipeline
# for overall example(all vertebrates motif in JASPAR will be processed)
conclusion <-
  atacPipe(
       # MODIFY: Change these paths to your own case files!
       # e.g. fastqInput1 = "your/own/data/path.fastq"
       fastqInput1 = system.file(package="esATAC", "extdata", "chr20_1.1.fq.gz"),
       fastqInput2 = system.file(package="esATAC", "extdata", "chr20_2.1.fq.gz"),
       # MODIFY: Set the genome for your data
       genome = "hg19")

## End(Not run)

esATAC documentation built on Nov. 8, 2020, 6:58 p.m.