import_novel_sj_reads_parallel: Import reads with novel splice junctions in parallel

In khembach/DISCERNS: DISCovery of unannotated Exons from RNa-seq Splice junction reads

Description

This functions takes a BAM file and a GRanges object with unannotated splice junctions as input and returns a GAlignments object with all reads from the BAM file that contain any of the novel splice junctions. The BAM files is read in parallel with mclapply using the specified number of cores.

Usage

import_novel_sj_reads_parallel(bam, yield_size = 2e+05, sj_unann, cores = 1)

Arguments

bam	Character string. The path to the BAM file.
yield_size	Integer scalar. Read the BAM file in chunks of this size.
sj_unann	GRanges object with unannotated splice junctions.
cores	Integer scalar. Number of cores to use. Default 1.

Value

GAlignments object with all reads from the BAM file that contain a novel splice junctions.

khembach/DISCERNS documentation built on June 23, 2020, 3:35 p.m.