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ay-lab / dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets
MIT License
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Question regarding enrich #90

Closed RomeroMatt closed 10 months ago

RomeroMatt commented 10 months ago

Hello, Thanks for the great tool. I have been learning how to use dchic on my existing Hi-C dataset. But I am a bit confused on one parameter. for the code below: Rscript dchicf.r --file input.txt --pcatype enrich --genome mm10 --diffdir conditionA_vs_conditionB --exclA F --region both --pcgroup pcQnm --interaction intra --pcscore F --compare F Do I need to run fithic and dloop prior to running --pcatype enrich? I interpreted the instructions as though you can look at gene enrichment in differential compartments, independent of loops. Am I misinterpreting this step? I was able to run all the steps prior to the optional ones, but when I run the enrich step, it asks for a bedpe file. Please see the error code below:

Finding gene enrichment for hPSC hPSC_SMPC Fetal_SMPC samples [1] "hPSC" "hPSC_SMPC" "Fetal_SMPC"
exclA is set to False, changing pcgroup from pcQnm to pcOri [1] "hg38_500000_goldenpathData" Error in file(file, "rt") : cannot open the connection Calls: geneEnrichment -> read.table -> file
In addition: Warning message: In file(file, "rt") : cannot open file 'DifferentialResult/hPSC_hPSC_SMPC_Fetal_SMPC_500kb/fdr_result/differential.intra_compartmentLoops.bedpe': No such file or directory Execution halted

Any insight would be helpful. Thanks!

-Matt

ay-lab commented 10 months ago

Hi,

Thanks for using the tool, and yes you can look at gene enrichment in differential compartments.

Please change the "--region both" option to "--region anchor" to do the same.

Let me know if you face any other issues.

RomeroMatt commented 10 months ago

Thank you! Looking back, I completely misinterpreted that option. I got it to work and I was able to make figures. Thanks!