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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

[Q]loop analysis takes long time #149

Closed jiangshan529 closed 3 months ago

jiangshan529 commented 3 months ago

Hi. I am ploting hic file on a bedpe file. the bedpe is tab seperated and has six columns, and it contains 2815 rows in total,

however, when I run a pileup on those loops it takes long time and it reported below messages, it seems most chromosome has more contact than my bedpe file of all chromosomes in total. Is this correct? Thanks! INFO:coolpuppy:('13', '13'): 215 INFO:coolpuppy:('4', '4'): 1621 INFO:coolpuppy:('8', '8'): 2182 INFO:coolpuppy:('9', '9'): 3882 INFO:coolpuppy:('18', '18'): 175 INFO:coolpuppy:('14', '14'): 4157 INFO:coolpuppy:('15', '15'): 5161

Phlya commented 3 months ago

What command do you run?

jiangshan529 commented 3 months ago

What command do you run?

coolpup.py aa_5k.cool group_none.bed --outname none.txt --flank 250000 --n_proc 16 --clr_weight_name "" plotpup.py --input_pups none.txt --not_symmetric --output none.pdf

Phlya commented 3 months ago

Try adding --features_format bedpe Your file ends with .bed, so coolpup.py assumes it's a .bed file, not .bedpe, so it calculates pairwise combinations of all left sides of the loops.

Also, the output is not in .txt format, just FYI...

jiangshan529 commented 3 months ago

thank you!

Phlya commented 3 months ago

I assume this is fixed then?

jiangshan529 commented 3 months ago

yes, thank you!

On Mon, Jun 10, 2024 at 6:11 AM Ilya Flyamer @.***> wrote:

I assume this is fixed then?

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