predict_jr_exon: Predict novel exons from reads with 2 junctions

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

Description

Novel exons are predicted from novel combinations of annotated splice junctions. Reads spanning two splice junctions are filtered from the set of all spliced reads. Each of the splice junction pairs are compared with the annotated splice junctions per transcript and already annotated splice junction pairs are removed. In the last step, the predicted exon that is defined by the two splice junctions is returned if it is contained within the boundaries of any annotated gene. This prevents the prediction of false positive exons from wrongly mapped reads.

Usage

predict_jr_exon(junc_reads, annotation)

Arguments

junc_reads	GAlignments object with junction reads.
annotation	List with exon and intron annotation as GRanges. Created with prepare_annotation().

Value

data.table with the coordinates of the predicted novel exon. It has 6 columns: seqnames, lend, start, end, rstart and strand

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