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Extracting methylation data from aligned BAMs #63

Open jameson-orvis opened 3 weeks ago

jameson-orvis commented 3 weeks ago

Ask away!

Hi! Quick question on extracting methylation data from aligned reads. Our raw bams have been methylation called already, so it seems like the easiest way to extract methylation information would be to use modkit on the aligned bams at {alias}.ns.bam. However, using "modkit pileup" gives errors of the form

failed to get modbase info for record 1977e594-f368-4232-a0de-cb0dea59e5b6:0079:0393, Bad Input: ML tag malformed

The code for pore-c-py seems like it is designed to pass modified bam information to the digested aligned output bams, so I am confused as to why this is happening. It may be an issue with the way I am calling modkit, but before I attempt troubleshooting further I want to ask if it should be possible to use modkit to extract methylation data from BAMs aligned from the pipeline, or if there is another preferred I should be processing methylation calls. Thank you!

sarahjeeeze commented 3 weeks ago

Hi thanks for letting us know this, the ML tag is not meant to be malformed we will investigate and get back to you