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kpalin avatar kpalin commented on August 16, 2024 1

Nothing to see there. The reads are "fine" but there are no methylation calls on them. The methylation likelihoods on 'C' bases are all low as you can see by parsing the ml tag. Currently absence of MM/MP tags mean "no methylation" for all sites.

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wdecoster avatar wdecoster commented on August 16, 2024

Hmm do you think it would be possible to share the cram file or post the first 5 lines of it?

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joanmarticarreras avatar joanmarticarreras commented on August 16, 2024

Hi Here is the header + 5 lines of ONT-CRAM ont-5.txt.

Thanks for having a look!

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wdecoster avatar wdecoster commented on August 16, 2024

Remarkable, the MM tag is there... let me think :)

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wdecoster avatar wdecoster commented on August 16, 2024

Is sharing the entire file possible?

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joanmarticarreras avatar joanmarticarreras commented on August 16, 2024

Hi @wdecoster ,

You can find the files in both this directions:

Thank you for having a look!

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wdecoster avatar wdecoster commented on August 16, 2024

So I've downloaded these files and indeed, there are reads (about 25%) that do not have the MM and MP tag. I'll tag @kpalin here, perhaps you have some insights to share? Did those reads not reach a certain quality/confidence score?

I could, of course, modify methplotlib to ignore reads without methylation tags, but I'd prefer to figure out first why these are absent.

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wdecoster avatar wdecoster commented on August 16, 2024

Okay thanks then I know how to handle these

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wdecoster avatar wdecoster commented on August 16, 2024

Things should be fixed in methplotlib-0.14.0!

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