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Arcadia-Science / 2023-amblyomma-americanum-txome-assembly

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Add more rules for evaluation & annotation #13

Closed taylorreiter closed 11 months ago

taylorreiter commented 11 months ago

Sorry this PR looks really messy because I reorganized a few things. This adds evaluation and annotation steps:

  1. "map" the reads back to the final transcriptome with salmon
  2. predict orfs & run busco using dammit. Dammit does more than just transdecoder by itself, and produces a cleaner set of files (along with CDS and amino acids, all with nice names). Because of this, I also removed transdecoder steps.