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google / deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
BSD 3-Clause "New" or "Revised" License
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Separate subreads for mixed samples? #68

Closed icemduru closed 1 year ago

icemduru commented 1 year ago

I have one SMRT Cell that contains two different samples with barcode information. Should I first separate my subreads based on the barcode info, or should I run DeepConsensus with the mixed subreads and then separate the reads with the barcode info from the HiFi output?

pgrosu commented 1 year ago

Hi Ilhan,

Yes you should split them first with lima, and here are a couple of reference posts regarding this:

Issue 32

https://github.com/PacificBiosciences/pbbioconda/issues/523

Hope it helps, Paul

icemduru commented 1 year ago

thanks ! and sorry for duplicate

icemduru commented 1 year ago

closed