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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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regarding HiC data in IMR90 #385

Closed tanasa closed 3 years ago

tanasa commented 3 years ago

Dear Nicolas, thank you again for a great package ! hope that my email finds you well.

as i am reading again your manuscript on HiC-Pro, and on HiTC :

http://bioconductor.org/packages/release/bioc/vignettes/HiTC/inst/doc/HiC_analysis.pdf

i was wondering if the LOOPS in IMR90 cell line (Dixon, Rao datasets) are available in "Dixon2012_IMR90" / "HiCDataHumanIMR90" or on the website (likely, i have missed it). thanks again, and best regards :)

nservant commented 3 years ago

Dear Bogdan, No, the package only contains the contact maps. The TADs are available on the original publication website here : http://chromosome.sdsc.edu/mouse/hi-c/download.html However, to my knowledge, the Dixon 2012 data was not resolutive enough to call loops. Hope it helps Nicolas

tanasa commented 3 years ago

thank you Nicolas ! have a good weekend, and ttyl ;)