Will trimming the reads mess up MM/ML tags

[weishwu]

I've run Dorado to do modbase calling in order to detect CpG methylation. Dorado output BAM which I then converted to FASTQ. I usually run NanoFilt to trim off the adapter-containing 5' (~40bp) and 3' (~20bp) ends before mapping and methylation calling. I wonder trimming after running Dorado will make the shortened read sequences incompatible with the info encoded in MM,ML tags. Thanks.

[ArtRand]

Hello @weishwu,

Indeed trimming the sequences will likely invalidate the MM/ML tags output by dorado. One option if you plan to use a tool like NanoFilt/Chopper is to follow up the trimming with modkit repair (docs), which will project the original MM/ML tags onto the trimmed sequences. You can always check if the MM/ML tags are correct by iterating through the BAM with pysam modified bases it will warn you if the tags are incorrect. modkit will do this as well in the logs when you use summary or a similar command. Hope this helps.

[weishwu]

@ArtRand Got it. Thanks!