findChrTails: findChrTails

In XHWUlab/PolyAtailor: a toolkit for analyzing poly(A) tail length dynamics from xxx RNA-seq data

Description

Each chromosome was traversed and PA sites were identified by a-rich at the end. Note that the BAM file needs to be indexed.

Usage

findChrTails(bamfile, which, what, count)

Arguments

bamfile	The path of bam file.
which	Refer to ScanBamParam parameters for Rsamtools for explanation.
what	Refer to ScanBamParam parameters for Rsamtools for explanation.
count	Boolean parameter. If count=T, the PA list after the count will be returned. There will be one more column of count in the PA list. If count=F, all PA site information is returned without counting.

Value

Returns a PA list annotated with chromosome information, chain orientation, and reference genomic coordinates.

XHWUlab/PolyAtailor documentation built on Dec. 28, 2021, 12:13 a.m.