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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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HiC-Pro iced normalized matrix show different bins from raw matrix #479

Open yuanyuanhe2021 opened 3 years ago

yuanyuanhe2021 commented 3 years ago

Hi, After iced normalization of raw matrix, I found the interaction bins(the first 2 cols of .matrix files) are different in the iced.matrix and raw matrix, like this:(I just showed the first 10 rows and the last 10 rows) 图片

图片 It seems like that the first 2 cols of ice.matrix and the raw matrix used to generate it are different. I was wondering if it is normal? because the first 2 cols are bin numbers, Would ice normalization change it? The HiC-Pro version I used is 2.11.4. Thank you very much.

nservant commented 3 years ago

Hi, Yes that's possible, as some data are filtered out before normalization, and bins to zéro are not written in the file. So, I'm not that surprise. Best