Different number of patterns for the same Hi-C matrix

[koszullab]

Different number of patterns for the same Hi-C matrix

[magnitov]

Hi @cmdoret,

I realized that for some reason I never came back to this issue. So, after a bit of investigation, I found out that there was a bug at the step before Chromosight, so those were actually not exactly the same Hi-C matrices. I believe this issue can be then closed, since the software is totally OK.

Best,
Mikhail

[cmdoret]

Hi @magnitov

Unfortunately, I could not reproduce your issue. I got consistent number of loops on the yeast, mouse and human datasets I tried (chromosight v1.6.0). That was just running chromosight detect -t6 sample.cool output.

Could you specify what command you used, or even better, if you have an example of a public dataset (e.g. from https://data.4dnucleome.org/) where you encountered this problem.

If it happens on your own data and you are comfortable with sharing it, you could send me the cool file by email ([email protected]) and I will investigate where the randomness comes from.

[cmdoret]

Thanks a lot for taking the time to come back to the issue ! Great news :)