To use a local copy of RefSeq as a transcript annotation database:

  1. Download the latest version of the RefSeq package from this NCBI ftp site.
  1. Choose a de novo transcriptome RNA-seq workflow.
  1. On the Transcript Annotation Database screen, select Add or Add Folder and select the file or folder for the RefSeq package that you downloaded in Step 1. Ignore the Transcript Annotation Options button on this screen. Since you are still using a RefSeq package, the default grep string and naming convention will be used automatically.
  1. Finish setting up and running the assembly as usual for this workflow type.

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