ThreeMostPairBam {APAlyzer} | R Documentation

## ThreeMostPairBam, extract 3 prime most alignment of a paired-end bam file

### Description

extract 3 prime most alignment of a paired-end bam file and saved into a new bam file.

### Usage

        ThreeMostPairBam(BamfilePath, OutDirPath, StrandType="NONE")

### Arguments

`BamfilePath` | file path of a bam file
`OutDirPath` | output folder path
`StrandType` | strand type of the bam file; "forward-reverse": read 1 forward but read 2 is reverse sequencing, "reverse-forward": read 2 forward but read 1 is reverse sequencing, and "NONE" is non-strand specific, Default is "NONE".

### Value

The function `ThreeMostPairBam()` return a single-end bam file containning 3 prime most alignment of the input paired-end file

### Author(s)

Ruijia Wang

### Examples

    ## Extract 3 prime most alignment of a paired-end
    ## bam file and saved into a new bam file
        library("pasillaBamSubset")

        ThreeMostPairBam (BamfilePath=untreated3_chr4(),
    						OutDirPath=getwd(),
    						StrandType='forward-reverse')

[Package APAlyzer version 1.8.0 Index]