Snakemake ChIP-seq Pipeline

If Nextflow is the pipeline manager favoured by genomics cores, Snakemake is the one favoured by people who think in Python. This one is for the Python thinkers.

What ChIP-seq Tells You That RNA-seq Can't

RNA-seq tells you which genes are expressed. ChIP-seq tells you WHY: where specific proteins are bound to the genome. H3K4me3 marks active promoters. H3K27me3 marks silenced regions. H3K27ac marks active enhancers. Map these marks and you understand the regulatory landscape.

The Most Critical Step: Input Control

Every ChIP-seq experiment needs an input control. Without it, you can't distinguish real binding from open chromatin artefacts. If someone gives you ChIP-seq without input controls, send it back.

Usage

snakemake --cores 8 --use-conda