# rMATS-cloud: Large-scale Alternative Splicing Analysis in the Cloud

## TL;DR

This paper introduces rMATS-cloud, a scalable cloud-based tool for analyzing alternative splicing in RNA-seq data, suitable for large-scale biomedical research.

## Contribution

The novel contribution is the development of a portable and scalable cloud version of the rMATS workflow for alternative splicing analysis.

## Key findings

- rMATS-cloud efficiently processes RNA-seq datasets with thousands of samples.
- The tool is compatible with multiple cloud platforms like Cavatica, Terra, and Seqera.
- It is well-suited for cloud storage capacities and large-scale data repositories.

## 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.