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)

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

Project Code	Award No	Project Name	Principal Investigator	Funder's Name	Funder Ref	Lead Dept
170547		The Wellcome Centre for Molecular Parasitology ( Core Support )	Andrew Waters	Wellcome Trust (WELLCOTR)	104111/Z/14/Z	III - Parasitology