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nanoporetech / modkit

A bioinformatics tool for working with modified bases
https://nanoporetech.com/
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modkit pileup - modified based code = 17802 #256

Open reJELIN opened 1 month ago

reJELIN commented 1 month ago

Hello there,

I just run modkit pileup on my freshly aligned RNA direct sample and after running it, the column "modified base code" is displaying 17802 for some rows ? By any chance would you know what does it mean ?

Best regards

ArtRand commented 1 month ago

Hello @reJELIN,

These codes are the ChEBI code for the base modification. In your case 17802 is pseudouridine. Only a few of the base modifications have single letter codes (you can find them in the specification, section 1.7).