fragment size and bin size

[Jin-Rui Xu]

Hi Dongjun,

I see almost all examples of constructbi that both fragment length and bin size are 200. 

I can understand why fragment length = 200, but what is the impact of changing bin size? Does it logically meaningful?

I ask because that I think in each bin is modeled by a mixture model to tell if it is a enriched bin, therefore should the bin size always be equal to fragment length?

Thanks.

Jinrui

[Dongjun Chung]

Hi Jinrui,

In general, bin size has only limited effects on the results, essentially spatial resolution and spatial correlation. Our rationale was that if bin size is similar to fragment length, two neighboring windows are "almost" independent, which is one of key assumptions of mosaics. In practice, it suffices that they are not significantly violated regarding the results. The only expection might be histone modifications, in which strong spatial correlation is expecdted. In this case, you might want to use MOSAiCS-HMM instead of MOSAiCS and MOSAiCS-HMM is already implemented in msoaics package as well.

Thanks,

Dongjun

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