ThreeMostPairBam: ThreeMostPairBam, extract 3 prime most alignment of a...

In RJWANGbioinfo/APAlyzer: A toolkit for APA analysis using RNA-seq data

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')

RJWANGbioinfo/APAlyzer documentation built on Dec. 6, 2024, 3:36 p.m.