prepIgBam: Extract alignments in intergenic regions from BAM files

In pliu55/pram: Pooling RNA-seq datasets for assembling transcript models

Extract alignments in intergenic regions from BAM files

Description

Extract alignments in intergenic regions from BAM files

Usage

prepIgBam(finbam, iggrs, foutbam, max_uni_n_dup_aln = 10,
    max_mul_n_dup_aln = 10)

Arguments

finbam	Full name of an input RNA-seq BAM file. Currently, PRAM only supports strand-specific paired-end data with the first mate on the right-most of transcript coordinate, i.e., 'fr-firststrand' by Cufflinks's definition
iggrs	A GenomicRanges object defining intergenic regions
foutbam	Full name of an output BAM file to save all alignment fell into intergenic regions
max_uni_n_dup_aln	Maximum number of uniquely mapped fragments to report per each alignment. Default: 10
max_mul_n_dup_aln	Maximum number of multi-mapping fragments to report per each alignment. Default: 10

Value

None

Examples

finbam = system.file('extdata/bam/CMPRep2.sortedByCoord.raw.bam',
                    package='pram')

iggrs = GenomicRanges::GRanges('chr10:77236000-77247000:+')

foutbam = tempfile(fileext='.bam')


prepIgBam(finbam, iggrs, foutbam)

pliu55/pram documentation built on March 30, 2024, 7:24 p.m.