identify_exon_from_sj: Identify a novel exon from a single novel splice junction

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

Description

Determine the size of the novel exon (unpaired internal splice junctions (SJ) and terminal junctions) based on the touching anntated exons and the RNA-seq reads. If a novel SJ touches either the start or end of an annotated exon and we have supporting reads with two SJs (the novel SJ and an annotated one) then we know the size of the novel exon and the coordinates of the neighbouring exons. If a novel SJ touches annotated exons on both ends, then the novel exon is either terminal or it overlaps with existing exons. In case of a terminal exon, the function returns NA for the location of the neighbouring exon.

Usage

identify_exon_from_sj(df, reads, txdb, cores)

Arguments

df	data.frame with novel splice junctions. Following columns are required: seqnames, start, end, strand and touching.
reads	GAlignments object. Reads that contain novel splice junctions, e.g. obtained with import_novel_sj_reads().
txdb	TxDb object, e.g. the "txdb" slot from the prepare_annotation() return object.
cores	Integer scalar. Number of cores to use. Default 1.

Value

data.frame with the coordinates of the identified novel exons from all splice junctions in df. It has 6 columns: seqnames, lend, start, end, rstart and strand.

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