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ay-lab / mustache

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
MIT License
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Resolution of calling loops #48

Open BenxiaHu opened 2 years ago

BenxiaHu commented 2 years ago

Hello, Thanks for developing this good tool to call chromatin loops. Our HiC sample just has ~150million valid pairs, do you think mustache can be used to call loops? and what resolution should be used? Best,

ay-lab commented 2 years ago

Hi, yes it can be used. To what extent it will miss loops, I can't be sure. 10kb or 20kb should be some resolutions that are reasonable although both would be stretching the data thin. 40kb/50kb should work but for finding loops it is not the ideal resolution. Please also consider FitHiC or other similar tools that compute enrichment wrt global background and are more lenient.