getSGFeatureCountsPerSample

features

BAM file with genomic RNA-seq read alignments

file_bam

Logical, <code>TRUE</code> for paired-end data,
<code>FALSE</code> for single-end data

paired_end

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

Number of cores available for parallel processing

cores


Obtain counts of compatible fragments for splice graph features.


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.

getSGFeatureCountsPerSample: Compatible fragment counts for splice graph features

Description

Usage

Arguments

Value