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smithlabcode / methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.
http://smithlabresearch.org/methpipe
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"hmr_plant" absent #168

Closed hchetia closed 4 years ago

hchetia commented 4 years ago

Hi I was not able to build "hmr_plant" command to run with the test dataset. Is it missing from methpipe 4.1.1?

terencewtli commented 4 years ago

Hi,

Could you show me the documentation you're reading for methpipe? In our manual, we have a section that discusses plant methylation and which programs to use. I believe hmr_plant is referring to our hyper_mr program, so you can try building that and running it on the Arabidopsis sample. However, the manual also mentions that you can find the blocks of hyper-methylated CpGs by inverting the methylation levels and running hmr on the sample.

hchetia commented 4 years ago

I was using the Readme.txt with the test dataset. Thanks for clearing that up. Hyper_mr works fine.

terencewtli commented 4 years ago

I see - I will edit that as well. Thanks for pointing that out!