Chromatin accessibility maps of chronic lymphocytic leukemia identify subtype-specific epigenome signatures and transcription regulatory networks
André F. Rendeiro*, Christian Schmidl*, Jonathan C. Strefford*, Renata Walewska, Zadie Davis, Matthias Farlik, David Oscier, Christoph Bock Chromatin accessibility maps of chronic lymphocytic leukemia identify subtype-specific epigenome signatures and transcription regulatory networks. Nat. Commun. 7:11938 doi: 10.1038/ncomms11938 (2016).
*Shared first authors
This repository contains scripts used in the analysis of the data in the paper.
A rendered version is available here.
To render the pdf version of the manuscript, run:
this requires in general a full latex installation.
In the paper website you can find most of the output of the whole analysis.
Here are a few steps needed to reproduce it (more than I'd want to, I admit):
- Clone the repository:
git clone firstname.lastname@example.org:epigen/cll-chromatin.git
- Install required software for the analysis:
pip install -r requirements.txt
If you wish to reproduce the processing of the raw data (access has to be requested through EGA), run these steps:
- Apply for access to the raw data from EGA.
- Download the data localy.
- Prepare Looper configuration files similar to these that fit your local system.
- Run samples through the pipeline:
looper -c metadata/project_config_file.yaml
- Get external files (genome annotations mostly):
make external_filesor use the files in the paper website (
- Run the analysis:
Additionaly, processed (bigWig and narrowPeak files together with a gene expression matrix) are available from GEO with accession number GSE81274.
If you wish to reproduce the plots from the analysis you can, in principle:
Not all parts of the analysis are possible to run as is, though. The TF network interence is based on a R package (PIQ) which is really hard to script runs in a system-independent way.