Skip to content

Latest commit

 

History

History
44 lines (27 loc) · 1.29 KB

README.md

File metadata and controls

44 lines (27 loc) · 1.29 KB
Raw

IRMB

Wrapper around nf-core/rnavar pipeline, to analyse RNA-seq (Illumina mRNA) data from GIAB

Reads are aligned using STAR, variants called with GATK HaplotypeCaller and annotated with ENSEMBL VEP

Installation

This script requires an activated Conda environment with:

It can be obtained with following commands:

conda create --yes --name irmb --channel conda-forge --channel bioconda --channel defaults nf-core singularity nextflow=22.10
conda activate irmb

# Then clone present repository and move inside it:
git clone https://github.com/tetedange13/IRMB.git
cd IRMB

Usage

Simply run:

./run_pipeline.sh

After pipeline complete, result files will be under rnavar sub-directory

Known limitations

  • Only chr22 from GRCh37 is analyzed

  • Recommended "base recalibration" step is skipped

  • A STAR index is built with a given read length that should match read length of processed FASTQ. Here iGenomes' index is 100 pb and GIAB data are 150 pb