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Understanding HiChIP data and interactions

Hi,

I am new to HiChIP data and I was wondering what is the best way to call interactions, using only reads within peaks, or using reads where at least one segment is a peak?

I have seen both approaches for HiChIP so I am not sure which is the way to go. Any thoughts are very much appreciated. Thank you!

hichip
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updated by Devon Ryan Devon Ryan • written by User 7754 User 7754

1 answer

Realistically speaking this will be dependent on how good the ChIP part was. If you got good enrichment then you can be more restrictive and require both reads to be in peaks. This will tend to cut down on lower probability contacts. If you got poorer enrichment then you'll probably need to be less restrictive just to have enough data.

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written by Devon Ryan Devon Ryan

Thanks very much Devon! By poor/good enrichment do you refer to enrichment of your protein of interest within the anchors, so for example if 80% of the anchors overlap your protein of interest?

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written by User 7754 User 7754

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