How to choose one chromosome for construction ?

Question

How to choose one chromosome for construction ?

liufuyan2016 opened this issue 2 years ago · 2 comments

liufuyan2016 commented 2 years ago

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

Answer 1 · 2023-01-03T20:06:44.000Z

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.

Answer 2 · 2023-03-12T12:37:40.000Z

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!