Effect of size of input region on FitHiC outputs

[Shanta]

Hi! I hope you are doing well. We have been using FitHiC to determine the significant interactions in our data for calling loops, and notice a difference in what is highly significant based on the size of the region we input (for example, a few Mb versus a full chromosome).  It seems that we get many more significant interactions when calling on smaller regions and filtering with a p-value threshold in comparison to larger regions. Have you had experience with this, and do you have any suggestions on how best to choose the size of the region and filtering for determining the true loops?

Thanks so much,

Shanta

[Ferhat Ay]

Hi Shanta, 

Due to several reasons (background estimation and multiple hypothesis testing, specifically), it is expected to have differences when you start with regions of different size. Or when you run it per chr vs genome-wide. 

The "best" choice is to input what you are interested in or ask only the question that you are interested in answering - just like any other hypothesis testing setting. If you are interested in identifying loops within a 5Mb region then only input that.

If you care about a specific chr then just use it and nothing else.

I hope this helps.

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