identify_exon_start: Determine the coordinates of a novel exon at the start of a...

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

Description

Given a set of reads that share a novel splice junction, determine the coordinates of a novel exon at the start of the splice junction. Only reads with the splice junctions (the novel SJ and an upstream SJ) are considered. If there are no reads with a second upstream SJ, take the range of the longest mapped part as an approximation for the coordinates of the novel exon (it probably is a terminal exon).

Usage

identify_exon_start(r, j_start, j_end, j_seqnames, j_strand)

Arguments

r	GAlignments object with reads that contain the novel splice junction.
j_start	Integer scalar. Start of the splice junction.
j_end	Integer scalar. End of the splice junction.
j_seqnames	Factor scalar. seqname of the splice junction.
j_strand	Factor scalar. Strand of the splice junction.

Value

data.frame with the coordinates of the predicted exon(s)

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