How to load the converted .hic file into Juicerbox

[Nuturetree]

The hic file regenerated by the order：
hictk load genome.sizes A1.hic -f validpairs -b 40000 < A1.allValidPairs

However the .hic file can not load into the juicerbox, how to resolved the err.
A1.zip

[robomics]

Hi!

I can open the file just fine on my laptop:

The .hic files generated by hictk are in .hic v9 format (the latest revision).
Older versions of juicebox cannot open these files, and I suspect this may be the problem in your case.

Can you try to open the files using juiceboxGUI (instead of normal Juicebox): https://github.com/aidenlab/JuiceboxGUI/releases/tag/v3.1.4

According to Juicebox's README newer versions of Juicebox will be published in the JuiceboxGUI repository.

[Nuturetree]

thanks
I have a other question, how to convert the validpairs to the matrix (Bin1 bin2 reads).

[robomics]

Did the above suggestion solve your issue?

hictk cannot directly convert validpairs to the COO format you are referring to.
However, once you have the validpairs loaded into a .hic or .cool file, then you can use hictk dump to view interactions in COO format.

See the docs for an example of how this can be done (you probably need to run something like hictk dump mymatrix.hic --resolution 10000).

[Nuturetree]

Could this feature be added, as the matrix format generated by HiC-Pro is also important for downstream analysis?

[robomics]

Can you paste here the head of the matrix file you are talking about?

If I remember correctly HiC-Pro matrix files are in one-based COO format already.
If this is the case (and I understand your question correctly), then you can load the pre-binned interactions using hictk load -f coo --one-based ... < file.matrix

[Nuturetree]

thanks