Problem with methcounts!

smithlabcode / methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.

http://smithlabresearch.org/methpipe

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Problem with methcounts! #176

Closed cheehowteo closed 2 years ago

cheehowteo commented 3 years ago

Dear author of methpipe,

Good day!

I am using methpipe for my methylation analysis and I have encountered a problem during methcounts stage. The error message I received was "could not find chrom: Contig0_pilon". I did supplied the reference contigs used for bismark with parameter -c and Contig0_pilon is in my reference contig fasta file. May I know how can I solve this problem?

Thank you.

Best regards, Teo

terencewtli commented 3 years ago

Hi, would you be able to provide more information? Maybe the full command that you used and a subset of your file/reference contig?

guilhermesena1 commented 2 years ago

closing due to inactivity but please feel free to reopen if you are still having the problem!