RNAseq-quantif-pipeline
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Download RO-CrateThis project is an analysis pipeline using Snakemake for RNAseq analysis in order to find differentially expressed genes. It has been widely tested on human RNA sequencing from an Illumina HiSeq but should work on most systems and many other species, provided the necessary resource files can be downloaded.
This pipeline is set for paired-end data only from Illumina HiSeq output files. The main steps of the pipeline are:
- Optionnal cleaning data with prinseq and/or cutadapt
- Alignment of reads on reference genome with STAR
- Counting features with HTSeq
- Detection of DGE genes with DESeq2
- Functional annotations with ClusterProfiler on GO and KEGG databases
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master @ 14d6641 (latest) Created 25th Sep 2025 at 15:32 by Hugo Lefeuvre
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Created: 25th Sep 2025 at 15:25
Last updated: 25th Sep 2025 at 15:32
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