search

open2c / cooltools

The tools for your .cool's
MIT License
140 stars 51 forks source link

Cooltools Dots problem in chicken genome with external mcool file #521

Closed pollicipes closed 6 months ago

pollicipes commented 6 months ago

Dear Cooltools developers,

I am trying to call loops using Dots in a chicken chromosome (galGal6 reference). I get to read my mcool into cooltools and get the expected_cis, but I am getting some IndexError after the cooltools.dots starts running. I have attached the code, the files and the log for the error. See: cooltools_chicken_example.zip

I have generated my mcool file using TADbit, @5_000 bp resolution, and it's Vanilla balanced. Maybe my mcool format is not correct?

Alternatively, could it also be because the chicken genome is not as well curated as mice or human, and has larger gaps? Any tips appreciated!

Thank you so much! Best, Juan

pollicipes commented 6 months ago

Update, for future reference: I found that the, apparently normalized/balanced, mcool matrix that TADbit produces does not have bad columns masked. So use the raw matrix and do the balancing from cooltools