predictExonsTerminal

<code>IRanges</code> of candidate internal exons

candidates

<code>IRangesList</code> with exonic regions from alignments

frag_exonic

<code>IRangesList</code> with introns implied by spliced
alignments

frag_intron

Minimum relative coverage required for exon prediction

relCov

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

Logical indicating whether counts of
compatible fragments should be included in elementMetadata column
&#147;N&#148;

include_counts

Logical indicating whether coverages for each
exon should be retained as an <code>IntegerList</code> in elementMetadata
column &#147;coverage&#148;. This allows filtering of features
using more stringent criteria after the initial prediction.

retain_coverage


Identify terminal exons based on candidate terminal exons and
compatible read coverage.


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.

predictExonsTerminal: Identify terminal exons

Description

Usage

Arguments

Value