Welcome to Snakemake RNA-seq pipeline documentation¶
Contents¶
This is the main documentation of the Snakemake RNA-seq pipeline. This pipeline takes single or paired-end mostly Illumina mRNA-seq reads and generates: 1. A quality report (multiQC format), 2. A mapping summary, 3. The gene raw read counts, 4. The gene scaled read counts
The gene raw counts can be directly used for differential gene expression with DESeq2 <https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html>.
A dedicated tutorial, available here <https://scienceparkstudygroup.github.io/rna-seq-lesson/06-differential-analysis/index.html> can be followed to perform this analysis.