Skip to content

DeplanckeLab/Chromatin_modules

Repository files navigation

This repository contains the code for the paper "Non-coding variants impact cis-regulatory coordination in a cell type-specific manner".

Note

Chromatin modules (CMs) represent sub-TAD hubs encompassing interactions between cis-regulatory elements, such as promoters and enhancers. CMs are charachterized by

  • interaction of active promoters with one or more active enhancers simultaneously (median of two-four enhancers),
  • preferential scaling at a sub-TAD level and therefore often being <100 kb in size (with median sizes ranging from 32 to 70 kb),
  • physical proximity of interacting elements within modules that show enrichment in 3D contacts,
  • deposition of histone modifications and binding of TFs in such regions in a coordinated fashion with transcriptional activity being a strong predictor of module formation. For more details, please refer to this review.

Explore CMs online!

This repository contains:

  1. Input data used for CM mapping
  2. Scripts for CM mapping with VCMtools, Clomics and PHM

Data preparation and CM mapping

I. Preparation steps:

  1. Clone the Chromatin modules repository
  2. Data preparation
    1. Download test data for LCLs, chr22, or use your own data
    2. Make sure to have ChIP-seq data (used in all methods) in the following format:
#Chr start end pid did strand sample_id_1 sample_id_2 ...
22 16192326 16192745 chr22:16192326:16192745 chr22:16192326:16192745 + -0.212 -0.175 ...
22 16204838 16205246 chr22:16204838:16205246 chr22:16204838:16205246 + -0.221 0.339 ...
22 16293852 16294075 chr22:16293852:16294075 chr22:16293852:16294075 + -0.038 0.0989 ...
  1. Genotype data in VCF files (used in PHM), see section 3 of this notebook on PHM-specific data preparation

II. CM mapping:

  1. Clomics
    1. Install Clomics-2.0.
    2. Adjust paths and parameters in the clomics_example.sh file.
    3. Run the script.
  2. VCMtools
    1. Adjust paths and parameters in the vcmtools_example.sh file.
    2. Run the script.
  3. PHM
    1. Install PHM.
    2. Prepare data in a PHM-specific format, following the steps explained in this notebook.
    3. Adjust paths and parameters in the 1.phm_example.sh file.
    4. Run the script.

III. CM exploration:

  1. Explore CMs from [...]CM.tracks.bed in IGV. Information on CM content, namely CM peak IDs, can be found in [...]CM.content.txt

About

Chromatin Modules across cell types.The code

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published