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Schick et al 2018 - Systematic functional characterization of BAF mutations yields novel intra-complex synthetic lethalities
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Systematic functional characterization of BAF mutations yields novel intra-complex synthetic lethalities

Sandra Schick, André F. Rendeiro, Bernd Boidol, Kathrin Runggatscher, Melanie Hinkel, Peter Májek, Loan Vulliard, Thomas Penz, Katja Parapatics, Christian Schmidl, Anna Ringler, Jörg Menche, Guido Boehmelt, Mark Petronczki, André Mueller, Christoph Bock, Stefan Kubicek

Paper: http://dx.doi.org/

Website: http://www.medical-epigenomics.org/papers/schick2018/

This repository contains scripts used in the analysis of the data in the paper.


Analysis of NGS data

Here are a few steps needed to reproduce the analysis:

  1. Clone the repository: git clone git@github.com:epigen/baf_complex.git
  2. Install required software for the analysis:make requirements or pip install -r requirements.txt

If you wish to reproduce the processing of the raw data (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108390), run these steps:

  1. Download the data localy from GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108390).
  2. Prepare Looper configuration files similar to these that fit your local system.
  3. Run samples through the pipeline: looper run metadata/project_config_file.yaml
  4. Get external files (genome annotations mostly): make external_files or use the files in the paper website (external folder).
  5. Run the analysis: make analysis

Additionaly, processed (bigWig and narrowPeak files together with a gene expression matrix) are available from GEO with accession number GSE108390.

Structural inference analysis

See the structuralInference folder.

Proteomics analysis

See the proteomics folder

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