Package: wnpp Severity: wishlist Subject: ITP: rosa -- Removal of Spurious Antisense in biological RNA sequences Package: wnpp Owner: Steffen Moeller <moel...@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
