BIROn - Birkbeck Institutional Research Online

    baerhunter: an R package for the discovery and anal-ysis of expressed non-coding regions in bacterial RNA-seq data

    Ozuna, A. and Liberto, D. and Joyce, R.M. and Arnvig, K.B. and Nobeli, Irene (2019) baerhunter: an R package for the discovery and anal-ysis of expressed non-coding regions in bacterial RNA-seq data. Bioinformatics , ISSN 1460-2059. (In Press)

    [img] Text
    BIOINF-2019-0830_Ozuna_etal_accepted_version.pdf - Author's Accepted Manuscript
    Restricted to Repository staff only until 16 August 2020.

    Download (419kB) | Request a copy

    Abstract

    Summary: Standard bioinformatics pipelines for the analysis of bacterial transcriptomic data com-monly ignore non-coding but functional elements e.g. small RNAs, long antisense RNAs or untrans-lated 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 au-tomates 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 Contact: i.nobeli@bbk.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

    Metadata

    Item Type: Article
    Additional Information: This is a pre-copyedited, author-produced PDF of an article accepted for publication following peer review. The version of record is available online at the link above.
    Keyword(s) / Subject(s): Bioinformatics, Gene expression, Genome annotation, Next-generation sequencing, RNA, Transcriptomics, RNA-seq, bacterial transcriptomics, non-coding RNA
    School: Birkbeck Schools and Departments > School of Science > Biological Sciences
    Divisions > Birkbeck Schools and Departments > School of Science > Biological Sciences
    Research Centres and Institutes: Bioinformatics, Bloomsbury Centre for (Closed), Structural Molecular Biology, Institute of (ISMB)
    Depositing User: Irene Nobeli
    Date Deposited: 20 Aug 2019 10:12
    Last Modified: 30 Jul 2020 00:14
    URI: http://eprints.bbk.ac.uk/id/eprint/28596

    Statistics

    Downloads
    Activity Overview
    2Downloads
    52Hits

    Additional statistics are available via IRStats2.

    Archive Staff Only (login required)

    Edit/View Item Edit/View Item