search

open2c / coolpuppy

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
MIT License
78 stars 12 forks source link

Recreating figure: And here is a real example of CTCF-associated loops in ES cells: #86

Closed mattbramble closed 2 years ago

mattbramble commented 2 years ago

Greetings, I've created a .clpy file, and I'm simply trying to recreate the figure stated in the heading:

"And here is a real example of CTCF-associated loops in ES cells"

on your walkthrough page.

I am unable to do this, although it seems like it should be a simple command.
I've tried various heatmap methods, but none seem to work properly. Thanks for any help.

Phlya commented 2 years ago

Please describe what exactly you tried, and what version of the tool you are using. (And what is not working, what is the error?)

mattbramble commented 2 years ago

Ah, thanks, I just got it to work using the walkthrough CLI page, which has the relevant examples. The following worked: plotpup.py --output plot_out.png --input input.clpy

mattbramble commented 2 years ago

I am, however, still wondering how to define the range of interaction distances that a heatmap will cover. For example, I need to include interactions of up to 800 kb. The output shows a range of perhaps 200 kb around the central peaks, assuming the squares that I see correspond to the set resolution of 5 kb of the input cooler file.

Phlya commented 2 years ago

Great, glad you figured it out!

To pileup larger areas, you need to set the --flank argument.

mattbramble commented 2 years ago

Thanks for the help, Ilya.