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baerhunter: An R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data

Ozuna, A; Liberto, D; Joyce, RM; Arnvig, KB; Nobeli, I; (2020) baerhunter: An R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data. Bioinformatics , 36 (3) pp. 966-969. 10.1093/bioinformatics/btz643. Green open access

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Abstract

SUMMARY: Standard bioinformatics pipelines for the analysis of bacterial transcriptomic data commonly ignore non-coding but functional elements e.g. small RNAs, long antisense RNAs or untranslated regions (UTRs) of mRNA transcripts. The root of this problem is the use of incomplete genome annotation files. Here, we present baerhunter, a coverage-based method implemented in R, that automates the discovery of expressed non-coding RNAs and UTRs from RNA-seq reads mapped to a reference genome. The core algorithm is part of a pipeline that facilitates downstream analysis of both coding and non-coding features. The method is simple, easy to extend and customize and, in limited tests with simulated and real data, compares favourably against the currently most popular alternative. AVAILABILITY: The baerhunter R package is available from: https://github.com/irilenia/baerhunter. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Type: Article
Title: baerhunter: An R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/bioinformatics/btz643
Publisher version: https://doi.org/10.1093/bioinformatics/btz643
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology
URI: https://discovery.ucl.ac.uk/id/eprint/10082522
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