RNAseq analysis

RNAseq pipeline

Start by running the nf-core/rnaseq pipeline.

Quick start

Example command (change cfc for binac on binac cluster):

#!/usr/bin/bash
nextflow run nf-core/rnaseq -r 1.4.2 -profile cfc \
--reads "Data/*{R1,R2}.fastq.gz" \
--genome 'GRCh37'

Normally, using all default values should be fine.

Known issues

• There is an incompatibility problem between GRCh38 and the default GTF file, so running with GRCh37 is still preferred.

Differential expression analysis

For differential expression analysis we use the qbic-pipelines/rnadeseq pipeline.

Quick start

Example command (change cfc for binac on binac cluster):

#!/usr/bin/bash
nextflow run qbic-pipelines/rnadeseq -r 2.1 -profile docker \
--gene_counts 'merged_gene_counts.txt' \
--input 'QXXXX_sample_preparations.tsv' \
--model 'linear_model.txt' \
--contrast_matrix 'contrasts.tsv' \
--project_summary 'QXXXX_summary.tsv' \
--multiqc 'MultiQC.zip' \
--software_versions 'software_versions.csv' \
--genome 'GRCh37'

Docker containers

After the release of rnadeseq 2.1, the docker containers were moved from Docker Hub to the GitHub Container Registry (ghcr) as Docker announced a change of free subscriptions. For all rnadeseq versions >2.1, this is reflected in the pipeline, so you don’t need to do anything.

For version 2.1, should you have trouble executing the pipeline because the container was removed from Docker Hub (this could for example lead to an error like “docker: Error response from daemon: manifest for qbicpipelines/rnadeseq:2.1 not found: manifest unknown: manifest unknown.”), please save the following code to a container.config:

process {
    withName: REPORT {
        container = 'ghcr.io/qbic-pipelines/rnadeseq:2.1'
    }
}

If you want to run a version <2.1, the container.config has to look like this:

process.container = 'ghcr.io/qbic-pipelines/rnadeseq:1.1.0'

The container link has to be adjusted to the version you want to run. You should just have to change the version number, but you can double-check on https://github.com/qbic-pipelines/rnadeseq/pkgs/container/rnadeseq if you are not sure if the link is correct.

Then, call this container.config when running the pipeline, like so:

qbic-pipelines/rnadeseq -r 2.1 -profile docker \
--many-many "params" \
-c path/to/container.config

Known issues

• No known issues

Reporting

The reporting is taken care of as part of the qbic-pipelines/rnadeseq pipeline. Check the previous section.