Differential interaction analysis

[goek...@googlemail.com]

Hi community,

Just successfully ran the dev version of HiC-Pro with nextflow (really great tool!). Now I am wondering what would be a solid workflow to determine differential interactions between two treatment conditions (each n=4-5)?

Particularly, I would appreciate pointers on which output files of HiC-Pro are particularly useful to continue with for that. I read that diffhic for instance suggests the use of raw count matrices.Where would those be located in the output? 

Any other basic workflow suggestions would also be appreciated. Currently, rerunning HiC-Pro to also output raw maps. Ultimately, one or more suggested workflows could be ideally be summarized in the FAQ section of the HiC-Pro GitHub.

Thanks,

Deniz

[赵华男/Herman Zhao]

Dear colleagues,

I am trying to build a Hi-C Pro Snakemake pipeline(https://github.com/hermanzhaozzzz/snakepipes_Hi-C). Currently, it appears to be working fine. And If you have any interest and suggestions, please feel free to contact me.

And welcome to contribute codes.

Yours,
Herman ZHAO

——————————————————————

ZHAO Hua-nan 

Ph. D. student

School of Life Sciences, Tsinghua University

Ph. D. Joint training

School of Life Sciences, Peking University

[nservant]

Thanks @Herman for your contribution ! 

@Deniz, it theory, you should have all counts table in the output of the nf-core-hic pipeline, either in txt or cool format.

I think that most of the tools should now support these two formats.

Best