cooltools virtual4c

[BenxiaHu]

hello cooltools developers,
cooltools virtual4c can generate a bigwig for a region of interest.

I just wonder whether cooltools virtual4c can generate a bigwig file for multiple regions (loci) of interest.

Best,
Benxia

[Phlya]

You have to run it one by one for each region you want... If I understand correctly what you are asking.

[Phlya]

Although it could be implemented to run for multiple regions at the same time, which would be much faster if you had a lot of regions. Is it something you need?

[BenxiaHu]

yes

[BenxiaHu]

I get an error.
the bigwig file can not be recongzed by IGV.
bad magnic number 0

[wangmhan]

Hello, I'm facing the similar problem: cannot generate bigwig files. The viewpoint was not working, though I specified it.
cooltools, version 0.7.1

here is my code:
cooltools virtual4c -p 4 --bigwig -o test coolers_library_group/sample.mcool::/resolutions/5000 chr15:61754325-63935880

Any suggestions? Thank you!

[gfudenberg]

hi @wangmhan -- the test cooler only has chr2 and chr17 so trying to export data for any other chromosome wouldn't work with that one!

There are some alternate coolers in: https://github.com/open2c/cooltools/tree/master/tests/data
You can see if virtual4c for the test region works:

cooltools/tests/test_virtual4c.py

Line 11 in aedd531

clr_path = op.join(request.fspath.dirname, "data/CN.mm9.1000kb.cool")