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nanoporetech / dorado

Oxford Nanopore's Basecaller
https://nanoporetech.com/
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Calling 0 length poly(A) tails #823

Closed eschiks closed 3 weeks ago

eschiks commented 4 months ago

I am interested in using Nano 3PSeq (https://www.nature.com/articles/s41592-022-01714-w) to sequence polyA'd and non-polyA'd transcripts. Previously this protocol used tailfindr for tail length calling, but this is no longer compatible with the new flow cells. I'm wondering if Dorado is capable of flagging transcripts lacking polyA tails and identifying custom adapter sequences like tailfindr was? And if it is not currently, could that functionality be added?

tijyojwad commented 4 months ago

Hi @eschiks - finding polyA with custom adapter sequencers was just released with dorado 0.7.0. You can find the documentation here - https://github.com/nanoporetech/dorado/blob/release-v0.7/documentation/PolyTailConfig.md#configuration-options

If dorado doesn't find polyA in a read, the pt:i tag will be missing in the output BAM record.