HiCCUPS vs HiCCUPSdiff

[arasim...@gmail.com]

Hi,

I have loops using HiCCUPS in my experimental and control Hi-C datasets, and detected ~4500 loops in the control, and ~6000 loops in the experimental dataset using the same default parameters (at 25kb resolution).  

However, when I run the HiCCUPSdiff between these two samples using the same parameters, I only get ~200 differential loops.

I am wondering what the reason is behind such a drastic difference of number of loops between the 2 datasets using only HiCCUPS vs. HiCCPSdiff (~1500 vs. 200).  

Thanks

Rasim

[Neva Durand]

HiCCUPSDiff uses strong criteria to call a differential loop.  To wit, it's not enough that the loop was not called originally in that data set; there must be an absence of enrichment.  So for example, if there is a loop in one dataset and no loop but a domain in the other, this would not be called as a differential loop.

Hope that helps.

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

[Neva Durand]

Just to clarify, HiCCUPSDiff does not look at domain annotation.  A better way to state it would be: If there is a loop called by HiCCUPS in one dataset and no loop called but weak local enrichment at that position in the other, this would not be called as a differential loop. 

Please see VI.e.4 of the supplement of Rao & Huntley et al Cell 2014 for more details.

[Rasim Barutcu]

Thank you very much for all the information.  This was really helpful.

Best,

Rasim