Universal Snakemake pipeline for processing paired-end RNA-seq data deposited at SRA

This pipeline will download the data, align the reads agaist any chosen genome and report gene counts as well as TPM for all samples.

Multiple runs (technical replicates) will be merged.

Setup

• clone this directory.
• download a RunTable from SRA that comprises teh samples of interest and place it into this directory.
• edit the file config.yaml providing the web locations of genome fasta and gff file.
• create a conda environment specified in sra_star_rsem.yaml.

conda env create --name sra_star_rsem --file sra_star_rsem.yaml

Running

activate the conda environment

conda activate sra_star_rsem

pre-flight checks

snakemake -np
snakemake --dag | dot -Tsvg > dag.svg

on local machine

with 16 cores

snakemake --cores 16

on the cluster

snakemake -j 999 --cluster-config cluster.json --cluster "sbatch -p {cluster.partition} -n {cluster.n} --mem {cluster.mem}"