Liquid-Chromatin-Hi-C

All code developed for the analysis of Liquid-Chromatin Hi-C assays.

A majority of code performs downstream analysis of Hi-C interaction matrices in cworld compatible HDF5 format:

• https://github.com/dekkerlab/cMapping
• https://github.com/dekkerlab/cworld-dekker

with ongoing devlopment for compatibility with cooler format:

• https://github.com/mirnylab/cooler

  Usage Examples

  Calculating Loss of Structure (LOS)

  
  # Scale control Hi-C matrix and predigested Hi-C matrix
  src/liquid_chromatin_HiC/scale.py -i control.hdf5
  src/liquid_chromatin_HiC/scale.py -i predigest.hdf5

Calculate 6 Mb cis percentage for scaled matrices

src/liquid_chromatin_HiC/hdf2RangeCisPercent.py -i control_scaleBy_x.hdf5 src/liquid_chromatin_HiC/hdf2RangeCisPercent.py -i predigest_scaleBy_x.hdf5

Calculate LOS from cis percent bedGraphs

src/scripts/LOS.R -i predigest_cispercent.bedGraph -m control_cispercent.bedGraph

### Calculating t<sub>1/2</sub>
```bash
# With all *LOS.bedGraphs from multiple timepoints in directory
src/scripts/make_LOS_table.R
# With output LOS table of all timepoints
src/scripts/get_half_life_exponential.R -i LOS_40kb.txt -f True

Contributing to liquid-chromatin-Hi-C

All contributions, bug reports, bug fixes, documentation improvements, enhancements, and ideas are welcome!

References

Houda Belaghzal, Tyler Borrman, Andrew D. Stephens, Denis L. Lafontaine, Sergey V. Venev, Zhiping Weng, John F. Marko, Job Dekker. (2019). Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C. bioRxiv

License

GNU General Public License v3.0