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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Possible methods for removing the multiple hits filter in HiC-Pro algorithm #447

Open Ti-Wen opened 3 years ago

Ti-Wen commented 3 years ago

Hello,

Thank you so much for developing HiC-Pro. It is a very nice tool to process Hi-C data. However, I think that there may be some limitations for analyzing the Hi-C data of organisms that consist of a high proportion of repetitive elements (or transposable elements) since the multiple hits filter shall discard some information of the interactions between transposons and genes. In my case, transposons take a proportion of 60%! So I wonder whether there is any method that I can modify the codes without ruining the tool. Thank you so much!

nservant commented 3 years ago

Hi, Did you try to simply turn off the multi-hits filtering ? by setting RM_MULTI=0 in the config ? N

Ti-Wen commented 3 years ago

Hi, No, I haven't tried this. I will try this method. Thank you very much! Ti-Wen