isoSeQL: comparing long-read isoforms across multiple datasets.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 41452740.
- Also identified by DOI 10.1093/bioinformatics/btaf680 and PMC identifier 12790818.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Long-read sequencing has made RNA isoform detection and characterization more accessible. While several bioinformatics tools have been developed to examine the data generated by these approaches, a major challenge in the field has been comparing isoform profiles across several samples. We developed isoSeQL, a tool for compiling long-read transcriptomic data, identifying common and unique isoforms across multiple samples, and extracting and visualizing various metrics. isoSeQL will augment approaches that utilize long-read sequencing to discover novel isoforms and to examine how isoforms vary across different experimental and biological conditions and cell types. We demonstrate how to use isoSeQL with publicly available datasets. isoSeQL is available on Github: https://github.com/christine-liu/isoSeQL and Zenodo:https://doi.org/10.5281/zenodo.15717809.
Medical subject headings
- Software
- Computational Biology
- Sequence Analysis, RNA
- RNA Isoforms