dorado Discrepancy between MinKNOW and dorado

I sequenced 48 isolates using kit SQK-RBK114-96. At first, I used basecalling on the PromethION device (P24; Joint Genome institute) and all looked good. However, it was version 4.12 of the model and I wanted to see if I could do better using 4.3. Also, I wanted methylation which I didn't ask for in the first place.

All looked good until I realized that when using dorado standalone, I got only a tiny fraction of the total reads demultiplexed. Most ended up in the unclassified bucket.

Am I missing something obvious here?

Thanks, Torben

Feb 26 '24 04:02 tnn111

Hi @tnn111, could you add some more detail please - the template should be a good guide as to what information to add - e.g. commands run.

Kind regards, Rich

Feb 27 '24 15:02 HalfPhoton

Hi @tnn111 - as @HalfPhoton can you post the cmd you ran and the version of dorado used?

Also, was demultiplexing and barcode trimming enabled in MinKNOW? Can you check the experiment logs?

Mar 05 '24 03:03 tijyojwad

@tnn111 do you have any updates?

Apr 02 '24 22:04 tijyojwad