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ay-lab / FitHiChIP

Statistically Significant loops from HiChIP data
MIT License
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is there any normalization step? #64

Closed jiangshan529 closed 2 years ago

jiangshan529 commented 3 years ago

Hi, I want to know if there's any normalization step in the differential analysis? What if two samples are hugely different in reads counts? Thanks

souryacs commented 3 years ago

Hi @jiangshan529 The differential ChIP (1D) bin analysis already takes into account the difference in sequencing depths, before attributing individual bins as differential or non-differential. On the other hand, differential HiChIP contacts are obtained by EdgeR, which also considers differences in sequencing depths to estimate the size factors.

jiangshan529 commented 3 years ago

Hi @jiangshan529 The differential ChIP (1D) bin analysis already takes into account the difference in sequencing depths, before attributing individual bins as differential or non-differential. On the other hand, differential HiChIP contacts are obtained by EdgeR, which also considers differences in sequencing depths to estimate the size factors.

Thanks for your reply. I have another question. When I use peaktoall mode, sometimes there are even less contacts than peaktopeak mode. I think there must be something wrong with it.