checkPairedEnd: Test whether a bam file is single-end or paired-end

In UofABioinformaticsHub/rnaCleanR: Calculate strandness information of a bam file

Description

Check the first 100000 first reads of the bam file to see whether it is single-end or paired-end

Usage

checkPairedEnd(file, yieldSize = 1e+05)

Arguments

file	the input bam file. Your bamfile should be sorted and have an index file located at the same path as well.
yieldSize	the number of reads to be checked, 100000 by default.

Value

return TRUE if the input file is paired end, and FALSE if it is single end

Examples

file <- system.file('extdata','s1.sorted.bam',package = 'strandCheckR')
checkPairedEnd(file)

UofABioinformaticsHub/rnaCleanR documentation built on Aug. 11, 2021, 11:51 p.m.