Bug#964191: ITP: rosa -- Removal of Spurious Antisense in biological RNA sequences
Package: wnpp
Severity: wishlist
Subject: ITP: rosa -- Removal of Spurious Antisense in biological RNA sequences
Package: wnpp
Owner: Steffen Moeller <moeller@debian.org>
Severity: wishlist
* Package name : rosa
Version : 1.0
Upstream Author : University of Dundee, UK
* URL : https://github.com/bartongroup/RoSA
* License : GPL-3.0+
Programming Lang: Python
Description : Removal of Spurious Antisense in biological RNA sequences
In stranded RNA-Seq experiments we have the opportunity to detect and
measure antisense transcription, important since antisense transcripts
impact gene transcription in several different ways. Stranded RNA-Seq
determines the strand from which an RNA fragment originates, and so can
be used to identify where antisense transcription may be implicated in
gene regulation.
.
However, spurious antisense reads are often present in experiments, and
can manifest at levels greater than 1% of sense transcript levels. This
is enough to disrupt analyses by causing false antisense counts to
dominate the set of genes with high antisense transcription levels.
.
The RoSA (Removal of Spurious Antisense) tool detects the presence of
high levels of spurious antisense transcripts, by:
* analysing ERCC spike-in data to find the ratio of antisense:sense
transcripts in the spike-ins; or
* using antisense and sense counts around splice sites to provide a
set of gene-specific estimates; or
* both.
.
Once RoSA has an estimate of the spurious antisense, expressed as a
ratio of antisense:sense counts, RoSA will calculate a correction to
the antisense counts based on the ratio. Where a gene-specific estimate
is available for a gene, it will be used in preference to the global
estimate obtained from either spike-ins or spliced reads.
Remark: This package is maintained by Steffen Moeller at
https://salsa.debian.org/med-team/rosa
Reply to: