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Is it possible to find out the PacBio chemistry from the PacBio Sequel BAM's header? E.g. whether it was produced with P5-C3 or P6-C4? I checked mine but I haven't found it but maybe it's hidden in one of the tags whose meaning I don't know yet, like SEQUENCINGKIT=100-861-800?

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According to PacBio Sequel BAM format manual, you can find information on the chemistry version in the header entries @RG (read group), tag DS (description), entry BASECALLERVERSION .

In case of future very PacBio-specific questions, you can contact Liz Tseng on Twitter (@magdoll), one of the most responsive PacBio developers. They also have a dedicated SeqAnswers forum, which is directly monitored by them and you are very likely to get a fast and accurate answer.

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  • $\begingroup$ I have 5.0.0.6236 for BASECALLERVERSION. Does it mean chemistry P5-C3 was used? $\endgroup$ Feb 9 '18 at 18:44
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    $\begingroup$ This surely means chemistry is higher than P4-C2 / 2.0, which is not supported in pbbam. The logical answer would be then yes, P5-C3 chemistry (or higher) was used. $\endgroup$
    – aechchiki
    Feb 12 '18 at 21:21

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