get_second_sj: Identify the second splice junction of a novel exon

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

Description

This function takes a set of novel splice junctions (SJ) as input and returns a data.frame with the location of the novel exon and the coordinates of the neighbouring exons. There are three different cases: 1) Novel SJs that touch an annotated exon with their start (5' end). 2) Novel SJs that touch annotated exons with their end (3' end). 3) Novel SJs that touch an annoated exon on both ends (5' and 3' end).

Usage

get_second_sj(junctions, reads, touching, txdb, gtxdb, ebyTr, cores)

Arguments

junctions	data.frame with novel splice junctions. Following columns are required: seqnames, start, end and strand.
reads	GAlignments object. Reads that contain novel splice junctions, e.g. obtained with import_novel_sj_reads().
touching	Character string. Which end of the novel splice junctions (parameter junctions) touches an annotated exon? One of "both", "start" or "end".
txdb	TxDb object, e.g. the "txdb" slot from the prepare_annotation() return object.
gtxdb	GRanges object. All genes from the txdb parameter, e.g. obtained with GenomicFeatures::genes(txdb).
ebyTr	GRangesList object. All exons per transcript of the txdb parameter, e.g. obtained with GenomicFeatures::exonsBy(txdb, by = "tx", use.names = TRUE).
cores	Integer scalar. Number of cores to use. Default 1.

Details

The three cases can be illustrated as follows:

1. Start touches annotation

   AAAA            annotated exon
      J---J        novel junction
    xxx---xx----x  read
           X----X  function return
   

2. End touches annotation

              AAA annotated exon
         J----J   novel junction
   xx---xx----xx  read
    X---X         function return
   

3. Both ends touch annotation

          AAAAA  annotated exon
   AAAA          annotated exon
      J---J      novel junction
     nn---xxxxx  possible transcript with novel exon nn at the 5' of the SJ
   xxxx---nn     possible transcript with novel exon nn at the 3' of the SJ
   

In case 3, we search for reads with two novel splice junctions that support a novel exon on either end of the SJ. If we do not find such reads, we check if the novel exon could be terminal, i.e. the first or last exon in the transcript. If yes, the novel exon does not have any touching annotated exon on that end and thus we cannot determine the end coordinate of the novel exon. As an approximation, we take the boundaries of the read with the longest mapping to the novel exon.

Value

data.frame with the coordinates of the 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.