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hiclib / pastis

Poisson-based algorithm for stable inference of DNA Structure
http://hiclib.github.io/pastis/
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How to choose one chromosome for construction ? #103

Open liufuyan2016 opened 1 year ago

liufuyan2016 commented 1 year ago

Dear, I only want to use one chromosome for construction. How to set inconfig.ini? Thank you!

gesinecauer commented 1 year ago

Hi, sorry for the slow response! You're saying that you have a whole-genome Hi-C dataset, but you only want to infer the structure of one chromosome, correct?

There is currently no way to do this via config.ini, unfortunately. I'd suggest filtering your Hi-C data prior to running PASTIS.

jinxin112233 commented 1 year ago

Hi, sorry for the slow response! You're saying that you have a whole-genome Hi-C dataset, but you only want to infer the structure of one chromosome, correct?

There is currently no way to do this via config.ini, unfortunately. I'd suggest filtering your Hi-C data prior to running PASTIS.

Hi Can you tell me how to get the counts.npy file? This question has been bothering me for a long time. I have .bam, .hic, .h5 files, but I don't know exactly how to convert them to .npy file. Thank you very much!