peaks2utr: a robust Python tool for the annotation of 3’ UTRs

Haese-Hill, W., Crouch, K. and Otto, T. D. (2023) peaks2utr: a robust Python tool for the annotation of 3’ UTRs. Bioinformatics, 39(3), btad112. (doi: 10.1093/bioinformatics/btad112) (PMID:36864613) (PMCID:PMC10008064)

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Abstract

Motivation: Annotation of non-model organisms is an open problem, especially the detection of untranslated regions (UTRs). Correct annotation of UTRs is crucial in transcriptomic analysis to accurately capture the expression of each gene yet is mostly overlooked in annotation pipelines. Here we present peaks2utr, an easy-to-use Python command line tool that uses the UTR enrichment of single-cell technologies, such as 10x Chromium, to accurately annotate 3’ UTRs for a given canonical annotation. Availability: peaks2utr is implemented in Python 3 (≥ 3.8). It is available via PyPI at https://pypi.org/project/peaks2utr and GitHub at https://github.com/haessar/peaks2utr. It is licensed under GNU GPLv3. Supplementary information: Supplementary data are available at Bioinformatics online.

Item Type:Articles
Additional Information:Funding: Wellcome Trust funded WHH and TDO (104111/Z/14/Z & A) and KC 218288/Z/19/Z.
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Crouch, Dr Kathryn and Haese-Hill, Dr William and Otto, Professor Thomas
Authors: Haese-Hill, W., Crouch, K., and Otto, T. D.
College/School:College of Medical Veterinary and Life Sciences > School of Infection & Immunity
Research Centre:College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Immunobiology
Journal Name:Bioinformatics
Publisher:Oxford University Press
ISSN:1367-4803
ISSN (Online):1460-2059
Published Online:02 March 2023
Copyright Holders:Copyright © 2023 The Authors
First Published:First published in Bioinformatics 39(3): btad112
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
170547The Wellcome Centre for Molecular Parasitology ( Core Support )Andrew WatersWellcome Trust (WELLCOTR)104111/Z/14/ZIII - Parasitology