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4dn-dcic / hic2cool

Lightweight converter between hic and cool contact matrices.
MIT License
67 stars 7 forks source link

Error in converting .hic to .cool #39

Closed rahmas36 closed 5 years ago

rahmas36 commented 5 years ago

Hi, I want to try out this new protocol called Cut-C, which combines Micro-C with Cut and Run to identify protein-centric interactions at high resolution. The authors uploaded .hic files on GEO which I wanted to convert to m.cool to visualize on HiGlass. However, when converting the .hic file to .cool I received this error message: ... This does not appear to be a HiC file; magic string is incorrect. I cannot load this file on Juicebox. What could be the problem? I attached the link to the file in question.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3587377

I downloaded the ftp link.

Thanks!

burakalver commented 5 years ago

Hi. It looks like the people who submitted the data to GEO used a wrong extension. The file looks like a pairs file, and not a hic file. That is why it can't be accepted by juicer or hic2cool. You should be ableo to use cooler to build a cool file. https://cooler.readthedocs.io/en/latest/