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smithlabcode / methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.
http://smithlabresearch.org/methpipe
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to-mr program for bsmap #147

Closed jinsooahn closed 3 years ago

jinsooahn commented 4 years ago

Hello, I tried to convert .bam file (from bsmap) into .mr using 'to-mr' command from both Major release 4.0.0 and methpipe-3.4.3, so I replaced the following command with my file name. $ to-mr -o Human_NHFF.mr -m bsmap Human_NHFF.bam

However, it returned the following message. "bsmap no longer supported [use general]"

According to the user manual, it should work. I am wondering if bsmap can be supported. Thanks,

mengzhou commented 4 years ago

Hi, thanks for using methpipe. We decided to integrate the support for bsmap with "general" because of some format incompatibility. Please use to-mr -m general with your file and see if it works fine.