atacRepsPipe: Pipeline for multi-replicates case paired-end sequencing data

In wzthu/ATACpipe: An Easy-to-use Systematic pipeline for ATACseq data analysis

Pipeline for multi-replicates case paired-end sequencing data

Description

The preset pipeline to process multi-replicates case study sequencing data. HTML report files, result files(e.g. BED, BAM files) and conclusion list will generated. See detail for usage.

Usage

atacRepsPipe(
  genome,
  fastqInput1,
  fastqInput2 = NULL,
  refdir = NULL,
  tmpdir = NULL,
  threads = 2,
  adapter1 = NULL,
  adapter2 = NULL,
  interleave = FALSE,
  createReport = TRUE,
  motifs = NULL,
  prefix = NULL,
  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	List scalar. 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. Each element in the fastqInput1 List is for a replicate It can be a Character vector of FASTQ files paths to be merged.
fastqInput2	List scalar. 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. Each element in the fastqInput1 List is for a replicate It can be a Character vector of FASTQ files paths to be merged.
refdir	Character scalar. The path for reference data being installed to and storage.
tmpdir	Character scalar. The temporary file storage path.
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.
createReport	Logical scalar. If the HTML report file will be created.
motifs	eitherPFMatrix, PFMatrixList, PWMatrix, PWMatrixList, default: vertebrates motif from JASPAR.
prefix	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.

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

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 <-
  atacRepsPipe(
       # MODIFY: Change these paths to your own case files!
       # e.g. fastqInput1 = "your/own/data/path.fastq"
       fastqInput1 = list(system.file(package="esATAC", "extdata", "chr20_1.1.fq.gz"),
                          system.file(package="esATAC", "extdata", "chr20_1.2.fq.bz2")),
       fastqInput2 = list(system.file(package="esATAC", "extdata", "chr20_2.1.fq.gz"),
                          system.file(package="esATAC", "extdata", "chr20_2.2.fq.bz2")),
       # 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 <-
  atacRepsPipe(
       # MODIFY: Change these paths to your own case files!
       # e.g. fastqInput1 = "your/own/data/path.fastq"
       fastqInput1 = list(system.file(package="esATAC", "extdata", "chr20_1.1.fq.gz"),
                          system.file(package="esATAC", "extdata", "chr20_1.2.fq.bz2")),
       fastqInput2 = list(system.file(package="esATAC", "extdata", "chr20_2.1.fq.gz"),
                          system.file(package="esATAC", "extdata", "chr20_2.2.fq.bz2")),
       # MODIFY: Set the genome for your data
       genome = "hg19")

## End(Not run)

wzthu/ATACpipe documentation built on Aug. 12, 2022, 7:38 a.m.