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 ...

GRAVI: Gene Regulatory Analysis using Variable Inputs

This is a snakemake workflow for:

1. Performing sample QC
2. Calling ChIP peaks
3. Performing Differential Binding Analysis
4. Comparing results across ChIP targets

The minimum required input is one ChIP target with two conditions.

Full documentation can be found here

Snakemake Implementation

The basic workflow is written snakemake, requiring at least v7.7, and can be called using the following ...