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EPPIcenter / mad4hatter

https://eppicenter.github.io/mad4hatter/
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Sequencer values #158

Open jodyphelan opened 3 months ago

jodyphelan commented 3 months ago

When running the pipeline Is there a list of valid values for --sequencer?

And how is this used in the analysis? I ran with --sequencer illuminaaaaa and it seemed to go through ok.

P.s. I think this might not be added into the example commands on the documentation yet.

bgpalmer commented 3 months ago

Hi Jody, thanks for logging an issue and pointing out the missing documentation. Currently, the sequencer options are miseq and nextseq, which roughly translates to 4-color vs 2-color and are used for determining which quality trimming method to use in cutadapt. We'll work on adding more sequencer options that translate to their respective color number and update the documentation. In the meantime, you should use --sequencer nextseq even if you ran your pipeline with a Novaseq.