please note : This pipeline is still in alpha stage. please use at your own risk
The aim of this pipeline ist to take of where nf-core/rnaseq leaves and add additional informations on top. The pipeline follows GATK guideline for variant calling in RNAseq. It then uses ASEReadCounter to retrive allele specific expression.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
The RNAseq_VAX pipeline comes with documentation about the pipeline, found in the docs/ directory:
This pipeline was written by Aron T. Skaftason (arontommi) but mostly cannibalised from nf-core/rnaseq