separateBamBystrand: Separate BAM files by strand

In BMILAB/scAPAtrap: Identification and Quantification of Alternative Polyadenylation Sites from Single-cell RNA-seq Data

Separate BAM files by strand

Description

Separate BAM files by strand

Usage

separateBamBystrand(samtools.path, input, thread = 12, ...)

Arguments

samtools.path	The path of the samtools.
input	The BAM file name.
thread	Number of CPU threads, default is 12.
...	Arguments passed to other methods and/or advanced arguments. Advanced arguments: verbose If 'TRUE' basic status updates will be printed along the way. logf If not NULL, then it should be a character string denoting a file name. Then message will be written to 'logf'. notRun Default is FALSE. If 'TRUE', the Shell commands inside this function will not run but output the commad line.

Value

String vector storing the path of the forward BAM file (<input>.forward.bam) and the reverse BAM file (<input>.reverse.bam)

Examples

samtools.path <- '/home/aa/miniconda2/envs/nar_env/bin/samtools'
input <- './data/demo.Uniq.sorted.dedup.bam'
## Not run: 
separateBamBystrand(samtools.path,input,24)

## End(Not run)
separateBamBystrand(samtools.path,input,24, notRun=TRUE)

BMILAB/scAPAtrap documentation built on Oct. 13, 2023, 2:36 a.m.