Dorado no-call for 6mA

[zhongzhd]

Hi,
When I was using Dorado to detect 6mA, I output the modification status of each site through Modkit and found that a large number of sites had a high rate of no-call results. According to the Modkit documentation, the undetected results are due to mismatches around the detection sites, such as CG turning into CH, which leads to a motif mismatch. However, 6mA detection should not be limited by motifs, so I am unclear why there is such a high proportion of no-call results.

[ArtRand]

Hello @zhongzhd,

Could you share the dorado command you used and the modified base model?

[zhongzhd]

Thanks for your reply, the code is as follows: "dorado-0.7.2-linux-x64/bin/dorado basecaller dorado-0.7.2-linux-x64/models/[email protected] pod5 --modified-bases 6mA --reference Ref.fa --secondary no --emit-moves --no-trim -x "cuda:1,2,3" > pod5_6mA.bam"

[ArtRand]

@zhongzhd that is strange. Could you tell me what modkit --version you have? Also could you extract the reads aligning to just this small window and attach them? Also do you see any indication in the Modkit logs that reads aren't being handled correctly?

[ArtRand]

@zhongzhd Did you use modkit call-mods on the modBAM before running modkit pileup?