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ay-lab / dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets
MIT License
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Can't get --bdgfile flag to work. #93

Closed RomeroMatt closed 7 months ago

RomeroMatt commented 7 months ago

Hello, Thanks again for the great tool. I've been able to get most everything to work. I am having difficulty with one thing and that is the viz option. I am trying to add RNA-seq bedgraph files to the html file, but it will not add them for some reason. My command is: Rscript dchicf.r --file input_merged_hPSC_hPSC_SMPC_Fetal_SMPC_500kb.txt --pcatype viz --diffdir merged_hPSC_hPSC_SMPC_Fetal_SMPC_500kb --genome hg38 --pcgroup pcQnm --bdgfile /data/dcHiC/bedgraph/bedgraphInfo_all.txt

My bedgraphInfo_all.txt file is a four column file with the layout as described in the help menu:

where my path is: path/to/folder/, ex: /data/dcHiC/bedgraph/ name: name of file w/o .bedgraph extension, ex: AP9-W17_1 type: bedgraph pos color:neg color: 250,0,0:0 The html is made, but just without the RNA-seq bedgraph file. Any help would be wonderful! -Matt
ay-lab commented 7 months ago

So, here is one of my demo bdgfile looks like - 

mESC.TPM.bedGraph       ES_TPM  bedGraph        255,55,118:0
NPC.TPM.bedGraph        NPC_TPM bedGraph        1,182,138:0

Please use 'bedGraph' instead of 'bedgraph' in the file and try again. I hope this will resolve the issue.

Sorry if I have mistyped it in the help menu.

RomeroMatt commented 7 months ago

Excellent! This worked - thanks a ton!