generateFinalBam: Generate a BAM file for called peaks with featureCounts and...

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

Generate a BAM file for called peaks with featureCounts and samtools

Description

Generate a BAM file for called peaks with featureCounts and samtools, which can be used by umi_tools to quantify peaks.

Usage

generateFinalBam(
  featureCounts.path,
  samtools.path,
  input,
  peakfile,
  thread = 12,
  ...
)

Arguments

featureCounts.path	The path of the featureCounts tool.
samtools.path	The path of the samtools.
input	BAM file.
peakfile	The path of the peaks.saf file generated by generateSAF.
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'.

Value

Generate final.bam file (final.bam) in the folder of the <input> dir.

Examples

## Not run: 
input <- './data/demo.bam'
peakfile <- './data/peaks.saf'
generateFinalBam(featureCounts.path, samtools.path, input, peakfile, 24)

## End(Not run)

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