Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python

• Published in: Bioinformatics (Oxford, England) Vol. 40; no. 12
• Main Authors: Kuehl, Malte, Wong, Milagros N, Wanner, Nicola, Bonn, Stefan, Puelles, Victor G
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 28.11.2024; Oxford Publishing Limited (England)
• Subjects: Applications Note; Availability; Bias; Gene expression; Gene Expression Profiling - methods; Gene mapping; Gene sequencing; Line interfaces; Packages; Python; Ribonucleic acid; RNA; Sequence Analysis, RNA - methods; Software; Source code; Transcriptome; Transcriptomes; Transcriptomics; Workflow
• ISSN: 1367-4811; 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btae700

Summary Transcript quantification tools efficiently map bulk RNA sequencing (RNA-seq) reads to reference transcriptomes. However, their output consists of transcript count estimates that are subject to multiple biases and cannot be readily used with existing differential gene expression analysis tools in Python. Here we present pytximport, a Python implementation of the tximport R package that supports a variety of input formats, different modes of bias correction, inferential replicates, gene-level summarization of transcript counts, transcript-level exports, transcript-to-gene mapping generation, and optional filtering of transcripts by biotype. pytximport is part of the scverse ecosystem of open-source Python software packages for omics analyses and includes both a Python as well as a command-line interface. With pytximport, we propose a bulk RNA-seq analysis workflow based on Bioconda and scverse ecosystem packages, ensuring reproducible analyses through Snakemake rules. We apply this pipeline to a publicly available RNA-seq dataset, demonstrating how pytximport enables the creation of Python-centric workflows capable of providing insights into transcriptomic alterations. Availability and implementation pytximport is licensed under the GNU General Public License version 3. The source code is available at https://github.com/complextissue/pytximport and via Zenodo with DOI: 10.5281/zenodo.13907917. A related Snakemake workflow is available through GitHub at https://github.com/complextissue/snakemake-bulk-rna-seq-workflow and Zenodo with DOI: 10.5281/zenodo.12713811. Documentation and a vignette for new users are available at: https://pytximport.readthedocs.io.