question about how to define the DRACH-motif

[mocherry]

Hi all,

we have done basecalling with Dorado with the following command:
dorado basecaller [email protected] --modified-bases m6A_DRACH > output bam.bam

Do I have to search for the DRACH sequence again in pilup or will only the potentially methylated bases in this context show up in the resulting output?

Thanks and best,
Matthias

[ArtRand]

Hello @mocherry,

You can use the --motif DRACH 2 argument to modkit pileup, the documentation describes how to do this. You'll need a reference sequence, but it will find the motif locations and output modification calls only at those positions.