Ozuna, A. and Liberto, D. and Joyce, R.M. and Arnvig, K.B. and Nobeli, Irene (2020) baerhunter: an R package for the discovery and anal-ysis of expressed non-coding regions in bacterial RNA-seq data. Bioinformatics 36 (3), pp. 966-969. ISSN 1460-2059.
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BIOINF-2019-0830_Ozuna_etal_accepted_version.pdf - Author's Accepted Manuscript Download (419kB) | Preview |
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 Faculties and Schools > Faculty of Science > School of Natural 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: | 02 Aug 2023 17:53 |
| URI: | https://eprints.bbk.ac.uk/id/eprint/28596 |
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