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magnitov / pentad

A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.
MIT License
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Rabl configuration #16

Open PengfeiInTuebingen opened 9 months ago

PengfeiInTuebingen commented 9 months ago

Hi Mikhail, Could we extract centromere or telomere clusters and calculate their compartment strength using panted? Best, Pengfei

magnitov commented 9 months ago

Hi @PengfeiInTuebingen,

Unfortunately, I do not this it is feasible with the current tool implementation.

Best, Mikhail

PengfeiInTuebingen commented 9 months ago

hi, thanks for your quick reply. do you have any recommendations for the rabl compartment analysis? pf

magnitov commented 9 months ago

I am not aware if any tools exist for this specific task. My go-to would be to use cooltools (https://github.com/open2c/cooltools) and pile-up the regions myself. See also here: https://www.biorxiv.org/content/10.1101/2023.07.15.549120v1.full.