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smithlabcode / methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.
http://smithlabresearch.org/methpipe
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Error running hmr & pmd #167

Closed hchetia closed 3 years ago

hchetia commented 3 years ago

Running into an error while identifying hypo-methylated regions in "test dataset". Snapshot attached. image

hchetia commented 3 years ago

Similar error with "pmd" image

andrewdavidsmith commented 3 years ago

Thanks @hchetia for this! This is an out-dated file format. I would not be surprised if we have forgotten to update something. Can you please give me the source of the file used here? If it was one of our example files, we will need to replace it ASAP. Our current methcounts output format is not the same as a bed format any more, because we now include the context of the site (e.g. CpG, CHH, etc.) and we don't use the redundant pair of start and end positions.

terencewtli commented 3 years ago

Hi @hchetia,

Thank you for pointing this out. I have just updated the methpipe test data. You can try redownloading and running hmr and pmd on the respective samples.

hchetia commented 3 years ago

Both hmr and pmd runs successfully on the new test data. Just want to add that the Readme.txt accompanying the test dataset should also be updated for the hmr_plant command.

terencewtli commented 3 years ago

I will fix that. Thank you!