MM tag preferred format for TAPS data

[jamesbaye]

Hello,

TAPS is a methyl-seq method where mC are converted into T.

In SAM spec, most of the mC examples highlight “C+m”, however C+m does not work off the shelf with TAPS data since the mC are represented in the SEQ as Ts and not Cs.

Alternatives to represent the mC mod could include T+m or N+m however these are not officially listed in the table of combinations. Is there any recommendation on which format to settle on?

Thanks,
James

[jkbonfield]

Apologies for the delay. Initially because I simply didn't know, and had never heard of TAPS, but then because I sadly got distracted and forgot to go back to this.

I'd think N+m is probably the way to go. The specification states:

"Note ‘N’ may be used to match any base rather than specifically an ‘N’ call by the sequencing instrument. This may be used in situations where the base modification is not a derivation of a standard base type".

(I wouldn't trust that T+m will work as it's could cause problems with validators. I haven't tried it, but I'd be surprised if it does work given the way the base counting works and there may well be tools that explicitly check compatibility of original and modified base type.)