findPAs: findPAs

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

findPAs(chrinfo, bamfile, resultpath, count)

Arguments

chrinfo	The path of chrinfo file.
bamfile	The path of bam file.
resultpath	The path of result file.
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.

Details

The findPAs function takes the information from the BAM file and the CHRinfo file that you input, calculates the PA site for each read based on the A-rich in the sequence, and consolidates and saves the PA sites information to the result path that you specify.

Value

Save the calculated PA site results to the result path that you specify.

See Also

[findAndAnnoPAs()] to quantitative tails without sequence algin.

Other poly(A) sites detection functions: findAndAnnoPAs()

Examples

bamfilepath = system.file("extdata", "./GV_algin/PAIso-GV1.sorted.bam",
package = "PolyAtailor", mustWork = TRUE)
chrinfopath = system.file("extdata", "./GV_algin/chrinfo.txt", package =
"PolyAtailor", mustWork = TRUE)
resultpath = "./"
test <- findPAs(chrinfo=chrinfopath,bamfile=bamfilepath,resultpath=resultpath)

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