how to prepare my input file?

[shenlinyong]

This software is really great, but I don't know how to prepare my input file? How should I make the input file from .HiC , cool or h5 format HiC file?

[ay-lab]

Hi @shenlinyong
Thanks for your query. FitHiC supports multiple input formats and provides utility functions to convert from existing Hi-C contacts.
Please check (https://github.com/ay-lab/fithic) section "Utilities". Within the source code repository "/fithic/utils/", you'll find the following utility functions:

1. HiCPro2FitHiC.py (Pre-processing. Generates --interactions, --fragments, and --bias inputs)
2. validPairs2FitHiC-fixedSize.sh (Pre-processing. Generates --interactions input)
3. createFitHiCContacts-hic.sh (Pre-processing. Generates --interactions input from .hic output)
4. HiCKRy.py (Pre-processing. Generates --bias calculation)

You can also check our nature protocol paper (https://www.nature.com/articles/s41596-019-0273-0) for step-by-step instructions on running FitHiC.

[shenlinyong]

Thank you very much for your answer. But my aim is to get genome-wide interactions between all chromosomes. The dump <chr1>[:x1:x2] <chr2>[:y1:y2] of the createFitHiCContacts-hic.sh script is mandatory, in which case I can only get interactions between two loci. Is there any way I can convert the data containing all the chromosomes in .hic format into one input file?

I am such an idiot, thanks again for your patient answer.