Flomics/rnaseq is a bioinformatics analysis pipeline used for RNA sequencing data.
The workflow processes raw data from FastQ inputs (FastQC, Trim Galore!), aligns the reads (STAR or HiSAT2), generates counts relative to genes (featureCounts, StringTie) or transcripts (Salmon, tximport) and performs extensive quality-control on the results (RSeQC, Qualimap, dupRadar, Preseq, edgeR, MultiQC). See the output documentation for more details of the results.
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 containers making installation trivial and results highly reproducible.
i. Install nextflow
ii. Install one of docker, singularity or conda
iii. Download the pipeline and test it on a minimal dataset with a single command
nextflow run Flomics/rnaseq -profile test,<docker/singularity/conda>iv. Start running your own analysis!
nextflow run Flomics/rnaseq -profile <docker/singularity/conda> --reads '*_R{1,2}.fastq.gz' --genome GRCh37See usage docs for all of the available options when running the pipeline.
The Flomics/rnaseq pipeline comes with documentation about the pipeline, found in the docs/ directory:
- Installation
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
- Troubleshooting
These scripts were originally written for use at the National Genomics Infrastructure, part of SciLifeLab in Stockholm, Sweden, by Phil Ewels (@ewels) and Rickard Hammarén (@Hammarn). Adapted to Flomics needs by Marta Pozuelo (@mpozuelo-flomics)
If you would like to contribute to this pipeline, please see the contributing guidelines.
For further information or help, don't hesitate to get in touch on Slack (you can join with this invite).