SamToBed: Convert SAM file to BED file

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

Convert SAM file to BED file

Description

This function is used to convert SAM file to BED file and merge interleave paired end reads, shift reads, filter reads according to chromosome, filter reads according to fragment size, sort, remove duplicates reads before generating BED file.

Usage

atacSamToBed(
  atacProc,
  reportOutput = NULL,
  merge = c("auto", "yes", "no"),
  posOffset = +4,
  negOffset = -5,
  chrFilterList = "chrM",
  samInput = NULL,
  bedOutput = NULL,
  sortBed = TRUE,
  minFragLen = 0,
  maxFragLen = 100,
  saveExtLen = FALSE,
  uniqueBed = TRUE,
  ...
)

## S4 method for signature 'ATACProc'
atacSamToBed(
  atacProc,
  reportOutput = NULL,
  merge = c("auto", "yes", "no"),
  posOffset = +4,
  negOffset = -5,
  chrFilterList = "chrM",
  samInput = NULL,
  bedOutput = NULL,
  sortBed = TRUE,
  minFragLen = 0,
  maxFragLen = 100,
  saveExtLen = FALSE,
  uniqueBed = TRUE,
  ...
)

samToBed(
  samInput,
  reportOutput = NULL,
  merge = c("auto", "yes", "no"),
  posOffset = +4,
  negOffset = -5,
  chrFilterList = "chrM",
  bedOutput = NULL,
  sortBed = TRUE,
  minFragLen = 0,
  maxFragLen = 100,
  saveExtLen = FALSE,
  uniqueBed = TRUE,
  ...
)

Arguments

atacProc	ATACProc-class object scalar. It has to be the return value of upstream process: atacBowtie2Mapping bowtie2Mapping
reportOutput	Character scalar report file path
merge	Logical scalar Merge paired end reads.
posOffset	Integer scalar The offset that positive strand reads will shift.
negOffset	Integer scalar The offset that negative strand reads will shift.
chrFilterList	Character vector The chromatin(or regex of chromatin) will be discard
samInput	Character scalar. SAM file input path.
bedOutput	Character scalar. Bed file output path.
sortBed	Logical scalar Sort bed file in the order of chromatin, start, end
minFragLen	Integer scalar The minimum fragment size will be retained.
maxFragLen	Integer scalar The maximum fragment size will be retained.
saveExtLen	Logical scaler Save the fragment that are not in the range of minFragLen and maxFragLen
uniqueBed	Logical scalar Remove duplicates reads in bed if TRUE. default: FALSE
...	Additional arguments, currently unused.

Details

The parameter related to input and output file path will be automatically obtained from ATACProc-class object(atacProc) or generated based on known parameters if their values are default(e.g. NULL). Otherwise, the generated values will be overwrited. If you want to use this function independently, you can use samToBed instead.

Value

An invisible ATACProc-class object scalar for downstream analysis.

Author(s)

Zheng Wei

See Also

atacBowtie2Mapping bowtie2Mapping atacFragLenDistr atacExtractCutSite atacPeakCalling atacBedUtils atacTSSQC atacBedToBigWig

Examples

library(R.utils)
library(magrittr)
td <- tempdir()
setTmpDir(td)

sambzfile <- system.file(package="esATAC", "extdata", "Example.sam.bz2")
samfile <- file.path(td,"Example.sam")
bunzip2(sambzfile,destname=samfile,overwrite=TRUE,remove=FALSE)
samToBed(samInput = samfile)

wzthu/wzzw documentation built on Aug. 13, 2022, 7:11 a.m.