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Updated: Jan 20, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
baerhunter: an R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data
A Ozuna1, D Liberto1, R M Joyce1
1Department of Biological Sciences, Institute of Structural and Molecular Biology, London, WC1E 7HX, UK.
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 And Implementation:
The baerhunter R package is available from: https://github.com/irilenia/baerhunter.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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