Final CpG of read detection

[benjamin-bfeng]

When looking through my ONT reads, I noticed that reads that end with a CG seem to not have an MM or ML tag associated with them. Is this expected behavior?

[ArtRand]

@benjamin-bfeng Do you mean that the final C is aligned to a reference CG or that the read is missing a modification call when the read sequence has a CG? Could you also tell me which model you're using (I would assume one of the CG models).

[benjamin-bfeng]

I mean the 2nd, if the read sequence ends in a CG (ie. NNNNNCG), I don't see a modification call associated with it. We used dorado to call 5mC and 5hmCs (dna_r9.4.1_e8_hac@v3.3). I now realize this might be a dorado question but thanks for the help anyways!

[ArtRand]

@benjamin-bfeng,

No problem. Could you paste a SAM record or attach a BAM file that is missing the modification call?