RNAseq analysis

RNAseq pipeline

Start by running the nf-core/rnaseq pipeline.

Quick start

• Latest stable release -r 1.4.2.

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

#!/usr/bin/bash
module purge
module load devel/singularity/3.4.2
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

• Latest stable release -r 1.1.0.

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

#!/usr/bin/bash
module purge
module load devel/singularity/3.4.2
nextflow run qbicsoftware/rnadeseq -r 1.1.0 -profile docker \
--rawcounts 'merged_gene_counts.txt' \
--metadata 'QXXXX_sample_preparations.tsv' \
--model 'linear_model.txt' \
--contrast_matrix 'contrasts.tsv' \
--project_summary 'QXXXX_summary.tsv' \
--multiqc 'MultiQC.zip' \
--quote 'QXXXX_signed_offer.pdf' \
--versions 'software_versions.csv' \
--report_options 'report_options.yml' \
--species Hsapiens

Known issues

• No known issues

Reporting

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