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ay-lab / dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets
MIT License
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pcatype enrich gene list error #96

Closed katecycho closed 6 months ago

katecycho commented 6 months ago

Hello!

I was able to successfully run dchic and thank you again for this tool. In running --pcatype enrich, I continue getting warning message Code: Rscript dchicf.r --file input.txt --pcatype enrich --genome hg38 --diffdir dir --exclA T --region anchor --pcgroup pcQnm --interaction intra --pcscore F --compare F Warning: There are way to many genes overlapping with the A compartment, the command line option has return an error! Please mannually upload the gene list.

This is output of a folder within the geneEnrichment folder. Screenshot 2024-03-11 at 10 40 21 AM

Could you please help me navigate through the files and how to extract the necessary information?

Thank you again so much for the help.

ay-lab commented 6 months ago

This is an issue from the https://toppgene.cchmc.org/enrichment.jsp side. dcHiC uses its API function to upload the gene list and perform enrichment, but if it is too big, it fails. I would suggest you to perform the gene enrichment using their site directly or using whatever your favorite tool is.

katecycho commented 6 months ago

Got it- thank you!!