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Oxford Nanopore's Basecaller
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Duplex basecalling using pair list - many pairs ignored? #91

Closed Delayed-Gitification closed 1 year ago

Delayed-Gitification commented 1 year ago

Hi,

I've made Pod5 files and a pairs list to run with dorado duplex.

However, the output seems to ignore many of the pairs in the list, only performing duplex basecalling on a small fraction of them.

I have validated that the pairs are true duplexes.

Is there any reason why this might be?

Thanks!

Oscar

vellamike commented 1 year ago

Hi, could you give some more details:

  1. What is the full command you are using (Just as a sanity check) ?
  2. What simplex model are you using to basecall?
  3. What does the read length distribution look like?
  4. What simplex accuracy are you observing for these reads?
iiSeymour commented 1 year ago

Dorado duplex will automatically pair your input reads for you in v0.3.0.