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jkimlab / msPIPE

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Can I use a genome that is not registered in the UCSC Genome Browser? #11

Open kondo-yuri opened 7 months ago

kondo-yuri commented 7 months ago

Can I use my own genome that is not registered in the UCSC Genome Browser?

mia110214 commented 7 months ago

Hello, thank you for your interest in msPIPE. However, it's not feasible to analyze an arbitrary genome sequence using msPIPE as it requires the use of the BSgenome R library.

kondo-yuri commented 7 months ago

I understood. Thanks for the quick reply.

kondo-yuri commented 7 months ago

Is it also impossible to skip the mapping process and use bam files?

Hello, thank you for your interest in msPIPE. However, it's not feasible to analyze an arbitrary genome sequence using msPIPE as it requires the use of the BSgenome R library.

heesun9 commented 7 months ago

@kondo-yuri It is possible to skip mapping and use your own bam file. Please refer to this README section. thank you.

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

and the output i get is : -Check all input .. ok

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