compi-rnaseq-pipeline

A compi RNA-Seq pipeline to perform differential expression using ballgown.

A Docker image is available for this pipeline in this Docker Hub repository. In order to run the pipeline locally, have a look at the required dependencies.

Running the pipeline with sample data

It is possible to test the pipeline using our sample data available here. Download the ZIP file and decompress it in your local file system. Then, to execute the pipeline using Docker, run the following command changing the /path/to/rna-seq-docker/data/ to the path where you have the decompressed data.

docker run --rm -it -v /path/to/rna-seq-docker/data/:/data singgroup/compi-rnaseq -pa /data/parameters

Pipeline results will be created in a directory called compi inside the main data directory.

Alternatively, it is also possible to execute the pipeline using Singularity. To do so, run the following command changing the /path/to/rna-seq-docker/data/ to the path where you have the decompressed data.

singularity run -B /path/to/rna-seq-docker/data/:/data docker://singgroup/compi-rnaseq -pa /data/parameters