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google / deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
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actc and kinetic data orientation #43

Closed gevro closed 2 years ago

gevro commented 2 years ago

Hi, actc is used to align subreads to ccs, but does actc reverse the orientation of kinetic (ip/pw) data in the BAM file it outputs? Or does Deepconsensus do this? I'm assuming either actc or Deepconsensus would have to do this to ensure that the kinetic data is in the correct orientation with the subreadstoccs alignment.

Thanks.

armintoepfer commented 2 years ago

Looking at two input subreads and their alignments or reading the PacBio BAM spec that you are well aware of, you'll figure out no aligner will change the orientation of tags.

pichuan commented 2 years ago

Hi @gevro , I'm closing this issue. If you have more questions, please feel free to open another issue or reopen. Thank you!