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open2c / coolpuppy

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
MIT License
77 stars 11 forks source link

Load/reoder chromosomes #131

Closed odovgusha closed 1 year ago

odovgusha commented 1 year ago

Hi, could you suggest a way to reorder the chromosomes in the cooler or load only particular chromosomes from the .cool file? I wanted to save RAM and try my script on some toy dataset. However, it seems that I cannot just plot some (present in the bed file) of the chromosomes from the cool file.

Many thanks!

Phlya commented 1 year ago

Sorry for the late reply. Hopefully you solved your problem by now, and in the future a better place for questions like this is the cooler or cooltools repository.

In case you still need to reorder chromosomes in a cooler, I actually recently wrote a tool for that, which is currently in a PR in cooltools: https://github.com/open2c/cooltools/pull/448 You can install the version from that branch of cooltools and use it.