Janus-a comprehensive tool investigating the two faces of transcription.

Barann, M., Esser, D., Klostermeier, U. C., Lappalainen, T., Luzius, A., Kuiper, J. W. P., Ammerpohl, O., Vater, I., Siebert, R., Amstislavskiy, V., Sudbrak, R., Lehrach, H., Schreiber, Stefan and Rosenstiel, Philip (2013) Janus-a comprehensive tool investigating the two faces of transcription. Bioinformatics, 29 (13). pp. 1600-1606. DOI 10.1093/bioinformatics/btt185.

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Supplementary data:

Abstract

Motivation: Protocols to generate strand-specific transcriptomes with next-generation sequencing platforms have been used by the scientific community roughly since 2008. Strand-specific reads allow for detection of antisense events and a higher resolution of expression profiles enabling extension of current transcript annotations. However, applications making use of this strandedness information are still scarce.
Results: Here we present a tool (Janus), which focuses on the identification of transcriptional active regions in antisense orientation to known and novel transcribed elements of the genome. Janus can compare the antisense events of multiple samples and assigns scores to identify mutual expression of either transcript in a sense/antisense pair, which could hint to regulatory mechanisms. Janus is able to make use of single-nucleotide variant (SNV) and methylation data, if available, and reports the sense to antisense ratio of regions in the vicinity of the identified genetic and epigenetic variation. Janus interrogates positions of heterozygous SNVs to identify strand-specific allelic imbalance.

Document Type: Article
Additional Information: Times Cited: 0 Barann, Matthias Esser, Daniela Klostermeier, Ulrich C. Lappalainen, Tuuli Luzius, Anne Kuiper, Jan W. P. Ammerpohl, Ole Vater, Inga Siebert, Reiner Amstislavskiy, Vyacheslav Sudbrak, Ralf Lehrach, Hans Schreiber, Stefan Rosenstiel, Philip
Research affiliation: OceanRep > The Future Ocean - Cluster of Excellence
Kiel University
Refereed: Yes
Open Access Journal?: No
DOI etc.: 10.1093/bioinformatics/btt185
ISSN: 1367-4803
Projects: Future Ocean
Date Deposited: 08 Jul 2014 08:50
Last Modified: 15 Jul 2019 09:46
URI: http://oceanrep.geomar.de/id/eprint/24816

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