Chapter 1 Introduction

This book is the primary documentation for running the GRAVI (Gene Regulatory Analysis using Variable Inputs) workflow. This workflow is managed using snakemake (>v7.7) for running locally or on any HPC, and is designed to minimally take one ChIP target under at least two conditions. There is no theoretical upper limit to the number of ChIP targets which can be analysed, although the practicalities of interpretation will dictate this.

Required additional inputs are:

  • A gtf with gene, transcript and exon-level annotations. The workflow has been tested extensively with Gencode annotations and these are preferred.
  • A blacklist should also be provided as a bed file. These can easily be obtained from here

In addition to \(\geq 1\) ChIP targets, optional input includes:

  • Differential Expression results from a single RNA-Seq experiment as a tsv/csv
  • Any type of genomic feature derived or obtained externally (*gtf)
  • HiC Interactions (*.bedpe)
  • Additional coverage tracks for visualisation, such as those produced by key histone marks (*bigwig)

The GRAVI workflow itself will

  • Annotate the genome using a custom, transcript-focussed approach
  • Identify peaks using macs2 callpeak
  • Perform differential binding analysis for each ChIP target & requested comparisons
  • Compare differential binding results across ChIP targets or samples (Pair-wise comparisons)
  • Perform enrichment analyses at all steps of the workflow

The primary output is a series of html pages generated from rmarkdown files, along with key figures and tables able to be shared amongst collaborators and incorporated directly into publications.