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ay-lab / dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets
MIT License
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Error: upper value must be greater than lower value Execution halted #52

Closed KunFang93 closed 1 year ago

KunFang93 commented 1 year ago

Hi,

Thanks for providing this useful tool! I meet a error 

Performing block wise correlation calculation   Error: upper value must be greater than lower value Execution halted

when I tried to run 

Rscript /data/kun/Softwares/dcHiC/demo/dcHiC_demo/scripts/dchicf.r --file input.NT_PT_RT.txt --pcatype cis --dirovwt T --cthread 1 --pthread 1

It looks like this error arises from generating chrY.pca.txt. I attached the files related to generate chrY.pca.txt. Thanks for your help!

chrY.txt chrY.precmat.txt chrY.bed.txt chrY.distparam.txt

Best, Kun

ay-lab commented 1 year ago

Hello,

In our analysis, we omitted chromosome Y. It is poorly mapped and compartments from this chromosome are of poor quality; we've had quite a few issues with this in the past as well. Would that work?

KunFang93 commented 1 year ago

Got it, I will try to remove chrY and re-run chic, thanks!

KunFang93 commented 1 year ago

Remove chrY from .matrix and .bed works, thanks!