Hi-C data analysis (Loop and domain calling)
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3 days ago
arsala521 ▴ 10

Hi,

I have some primates HI-C data from NCBI GEO. I step-by-step followed HOMER Hi-C analysis pipeline to determine TADs and loops from the Hi-C reads. Theoretically, there are multiple loops in a TAD and number of loops are always higher than TADs. However, I got TADs in much higher number than loops.

Does someone have any idea why is it happening? Should I try using some tool other than HOMER for TAD and loop calling?

Thank you

calling and Hi-C HOMER domain Loop • 115 views
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