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ay-lab / dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets
MIT License
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File for -repParams missing chr Y #20

Closed esebesty closed 3 years ago

esebesty commented 3 years ago

I'm running an analysis where I have no replicates, and was following the wiki instructions. However, analysis of chr Y failed, and I found out that it fails at this line, as the humanparams.txt file does not contain info on chr Y. This info also seems to be missing from the mouse file. Is this intentional (I'm not an expert on HiC analysis)?

ay-lab commented 3 years ago

Hello,

Yes— in our analysis, we omitted chromosome Y. It is poorly mapped and compartments from this chromosome generally tend to look pretty bad. You can create your own replicate parameters with multiple chrY samples or simply omit it.

esebesty commented 3 years ago

OK, thanks!