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aidenlab / Juicebox

Visualization and analysis software for Hi-C data -
https://aidenlab.org/juicebox
MIT License
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Bin randomization #809

Closed sa501428 closed 5 years ago

sa501428 commented 5 years ago

Randomization errors encountered: no map found, two different maps found This statement should only be printed if the bin randomization flag is passed in, not by default.

zyqfrog10 commented 5 years ago

Hello,

Recently I transformed HiCPro output into .hic with a fragment file. Everything ran smoothly and the results could be loaded into juicebox without any problem. But when I checked the log file, there was one line "Randomization errors encountered: 0 no map found, 0 two different maps found."

I'm trying to understand the randomization process here. Looks like in 'Preprocessor.java', initially it is set as 'allowPositionsRandomization = false', and I did't see anywhere this boolean got changed. So the position randomization seems like not triggered ever letting 'noMapFoundCount = 0, and mapDifferentCount = 0.' I may miss something here. Could you help explain this? Thanks, Ada

sa501428 commented 5 years ago

Hi @zyqfrog10 bin randomization is not performed by default and requires specific flags. There are no issues with your file.

zyqfrog10 commented 5 years ago

Thanks so much for the quick clarification! That confirms my thinking.