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ay-lab / dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets
MIT License
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`numberclust` parameter #51

Closed YichaoOU closed 1 year ago

YichaoOU commented 1 year ago

Hi,

The default value for numberclust is 1, if I increase it to 2, then no more significant compartments, which is what I want.

My question is that, based on your description on Compartment clustering, it makes sense to remove lone differential compartments. But is it OK to just change numberclust and keep distclust as default (-1)?

Thanks, Yichao

ay-lab commented 1 year ago

Yes, please use distclust as -1, you can ignore that part. If you want to cluster the differential compartment and merge continuous lone peaks, you can simple use the merge option from bedtools. In our Nat comm dcHiC paper, we never merged the lone peaks and used as it is.

YichaoOU commented 1 year ago

Thanks!