splicesiteOverlap

splicesites

Character vector indicating whether the spliced boundary
is to the left (&#147;L&#148;) or right (&#147;R&#148;) of the splice site

side

<code>IRangesList</code> of exonic regions, one entry
per fragment

frag_exonic

<code>IRangesList</code> of introns, one entry per fragment

frag_intron

Character string indicating whether considered fragments
should be all that overlap the splice site (&#147;all&#148;), those
that are spliced at the site (&#147;spliced&#148;) or those that are
not spliced, i.e. extend into the adjacent intron (&#147;unspliced&#148;)

include

Logical indicating whether counts or indices of
compatible fragments should be returned

counts


Identify fragments with alignments extending across exon/intron boundaries.


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.

splicesiteOverlap: Compatible fragment counts for splice sites

Description

Usage

Arguments

Value