prepareChIPs

This is a simple snakemake workflow template for preparing single-end ChIP-Seq data. The steps implemented are:

1. Download raw fastq files from SRA
2. Trim and Filter raw fastq files using AdapterRemoval
3. Align to the supplied genome using bowtie2
4. Deduplicate Alignments using Picard MarkDuplicates
5. Call Macs2 Peaks using macs2

A pdf of the rulegraph is available here

Full details for each step are given below. Any additional ...