Mechanistic InteGrative aNalysis Of rNa-seq data
This repository contains all the necessary code to execute MIGNON, a bioinformatic workflow for the analysis of RNA-Seq capable of integrating genomic and transcriptomic data into mechanistic signaling circuits. It covers the whole process using state-of-the-art tools and is deployable in under different computational environments. By using an in-silico knockdown strategy, it calculates the signaling circuit activities from gene expression and loss-of-function variants using raw reads as input. It is written using the Workflow Description Language (WDL) and can be executed using cromwell and docker (or other engine able to run docker containers). For more information about MIGNON, please visit the documentation:
Users with experience on workflow managers and containers can directly clone and execute the dry run of the workflow if they already have Git, Java (v1.8.0) and docker installed. This can be done by executing the following commands on your terminal:
git clone https://github.com/babelomics/MIGNON.git
cd MIGNON
bash runMignonExample.sh
After completing the dry runs, the results of the pipeline can be found at the dry_run/cromwell-executions directory.
If you use MIGNON, please cite:
Garrido-Rodriguez M, Lopez-Lopez D, Ortuno FM, Peña-Chilet M, Muñoz E, Calzado MA, Dopazo J. A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways. PLoS Comput Biol. 2021 Feb 11;17(2):e1008748. doi: 10.1371/journal.pcbi.1008748. Epub ahead of print. PMID: 33571195.