predictCandidatesTerminal

junctions

<code>IRanges</code> of genomic regions with minimal read
coverage required for internal exon prediction

islands

Character string indicating whether terminal exons
should be identified to the left (&#147;exon_L&#148;) or right
(&#147;exon_R&#148;) of provided splice junctions

type


Identify candidate terminal exons based on previously identified
splice junctions and regions with minimal read coverage required
for terminal exon prediction.


internal

RNA-seq data are informative for the analysis of known and
novel transcript isoforms. While the short length of RNA-seq
reads limits the ability to predict and quantify full-length
transcripts, short read data are well suited for the analysis
of individual alternative transcripts events (e.g. inclusion
or skipping of a cassette exon). The SGSeq package enables the
prediction, quantification and visualization of alternative
transcript events from BAM files.

predictCandidatesTerminal: Identify candidate terminal exons

Description

Usage

Arguments

Value