Year: 2025
Type: article
Abstract: Although gene expression analysis pipelines are often a standard part of bioinformatics analysis, with many publicly available cloud workflows, cloud-based alternative splicing analysis tools remain limited. Our lab released rMATS in 2014 and has continuously maintained it, providing a fast and versatile solution for quantifying alternative splicing from RNA sequencing (RNA-seq) data. Here, we present rMATS-cloud, a portable version of the rMATS workflow that can be run in virtually any cloud environment suited for biomedical research. We compared the time and cost of running rMATS-cloud with two RNA-seq datasets on three different platforms (Cavatica, Terra, and Seqera). Our findings demonstrate that rMATS-cloud handles RNA-seq datasets with thousands of samples, and therefore is ideally suited for the storage capacities of many cloud data repositories. rMATS-cloud is available at https://dockstore.org/workflows/github.com/Xinglab/rmats-turbo/rmats-turbo-cwl, https://dockstore.org/workflows/github.com/Xinglab/rmats-turbo/rmats-turbo-wdl, and https://dockstore.org/workflows/github.com/Xinglab/rmats-turbo/rmats-turbo-nextflow.
Language: English
Topic: RNA Research and Splicing
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,850
Awards: G1308892644, G1403651065, G320128651, G4428245006, ProteoSeq - An Integrative Computational Framework for Proteotranscriptomics, Targeting alternative isoform variation for TCR discovery in platinum-resistant ovarian cancer, Targeting alternative splicing for TCR discovery in small cell carcinomas, G8735138472, G9000006420, G9000062113, G9000063289, G9000071351, G9000127251
OpenAlex ID: W4410198171