Sara Sdelci, André F. Rendeiro, Philipp Rathert, Gerald Hofstätter, Anna Ringler, Herwig P. Moll, Wanhui You, Kristaps Klavins, Bettina Gürtl, Matthias Farlik, Sandra Schick, Freya Klepsch, Matthew Oldach, Pisanu Buphamalai, Fiorella Schischlik, Peter Májek, Katja Parapatics, Christian Schmidl, Michael Schuster, Thomas Penz, Dennis L. Buckley, Otto Hudecz, Richard Imre, Robert Kralovics, Keiryn L. Bennett, Andre Müller, Karl Mechtler, Jörg Menche, James E. Bradner, Georg E. Winter, Emilio Casanova, Christoph Bock, Johannes Zuber, Stefan Kubicek
This repository contains scripts used in the analysis of the data in the paper.
Here are a few steps needed to reproduce it (more than I'd want to, I admit):
- Clone the repository:
git clone git@github.com:epigen/mthfd1.git
- Install required software for the analysis:
make requirements
orpip install -r requirements.txt
If you wish to reproduce the processing of the raw data, run these steps:
- Download the data from GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE105786).
- Prepare Looper configuration files similar to these that fit your local system.
- Run samples through the pipeline:
make preprocessing
orlooper run metadata/project_config_file.yaml
- Run the analysis:
make analysis
Additionaly, processed (bigWig and narrowPeak files together with a gene expression matrix) are available from GEO with accession number GSE105786.