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

• Published in: Bioinformatics (Oxford, England) Vol. 39; no. 3
• Main Authors: Haese-Hill, William, Crouch, Kathryn, Otto, Thomas D
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.03.2023
• Subjects: 3' Untranslated Regions; Applications Note; Gene Expression Profiling; Software
• ISSN: 1367-4811; 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btad112

Abstract Summary Annotation of nonmodel 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 10× Chromium, to accurately annotate 3′ UTRs for a given canonical annotation. Availability and implementation 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.