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jkimlab / msPIPE

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error calling methylation with non UCSC genome #14

Open JUxueML opened 3 months ago

JUxueML commented 3 months ago

Hello, I've been trying to use my own bam file and just use the pipeline for the methylation calling and the following steps but I still get an error asking for the UCSC_NAME. Im running this command : msPIPE.py --param params_format.conf --out ../output_msPIPE/ --skip_trimming --program bismark --skip_mapping

command: msPIPE.py --param params_format.conf --out ../output_msPIPE/ --skip_trimming --program bismark --skip_mapping and the output i get is : -Check all input .. ok

Check reference *** "UCSC_NAME" is mandatory option (UCSC genome name). Please check the parameter file

Is there a way to circumvent this issue and work with a genome not in the UCSC GB. I also tried to give the folders for the methylation calls i did on my own with bismark but still get the same issue

mia110214 commented 2 months ago

Hello, I apologize for the delay in response. Due to the library currently used in msPIPE, it is difficult to use when UCSC genome name is not available.