get_SRcount: Count splice junction reads from BAM files

In hyochoi/SCISSOR: Shape changes in selecting sample outliers in RNA-seq

Count splice junction reads from BAM files

Description

Extract splice junction counts from BAM files for the provided regions.

Usage

get_SRcount(BAMfiles, caseIDs = NULL, regions = NULL, print.proc = FALSE)

Arguments

BAMfiles	a list of BAM file names
caseIDs	a list of case IDs in order of BAMfiles
regions	genomic regions to read formatted as "chr1:1-100,200-300:+". See also build_gaf.

Examples

regions="chr1:1-100,200-300:+"
start_time = Sys.time()
countPileup = read_SRcount(BAMfiles=BAMfiles,caseIDs=caseIDs,regions=regions)
end_time = Sys.time()
end_time - start_time

hyochoi/SCISSOR documentation built on July 6, 2022, 6:59 a.m.