predictJunctions

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

frag_exonic

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

frag_intron

Minimum fragment count required for a splice
junction to be included. If specified, argument <code>alpha</code> is ignored.

min_junction_count

Minimum splice frequency required for a splice junction
to be included

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

retain_coverage


Identify splice junctions from genomic RNA-seq read alignments.


internal

Predict splice junctions and exons from BAM files and obtain
compatible read counts and FPKMs. Identify splice events and
estimate relative usage of splice variants based on compatible
read counts at event boundaries.

predictJunctions: Identify splice junctions

Description

Usage

Arguments

Value