prepIgBam {pram} | R Documentation

## 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)

[Package pram version 1.4.0 Index]