Check the normalizations available in a hic file?

Question

[rls_08]

Haven't found a good CLI tool that can query information on a hic file that will output the available normalization factors/ or values in a .hic file. The closer tool to read metadata in a .hic file is read_hic_header.py ; but it does not output information on the available normalizations.

Answer 1

[cmdcolin]

It's a bit odd to use a js tool for this but hic-straw (js) can do it. it seems like there's a bug with the latest but works if you pin the a older version via npm install

$ npm install -g "hic-straw@v2.0.3" 
$ npm install -g "node-fetch@^2.0.0"       
$ straw intra_nofrag_30.hic --norms 
[ 'NONE', 'VC', 'VC_SQRT', 'KR' ]

[rls_08]

thanks. I just found out that juicer_tools can also do it straight in the terminal

Answer 2

[Jim Robinson]

I'll look into this, if you want to track progress follow this git issue: https://github.com/igvteam/hic-straw/issues. As Colin suggests pinning a previous version should fix the issue, I suggest version 2.0.5. I suspect commit b7516811a47f5094cd4a7d8c3a5cb3cc0cafa913 is the culprit here, which changed the package type to "module".

There are "straw" tools for extracting hic information in various languages here: https://github.com/aidenlab/straw. Have you tried opening an issue in that repository?

Answer 3

[rls_08]

I just found out that you can run java -jar juicer_tools.jar validate your-hic-file.hic and it will give you some information, including the normalization values/factors available.