The topic RNA-Seq de novo transcriptome workflow provides a list of steps for generating output in the form of contigs. You may use these contigs as reference sequences in the RNA-Seq reference-guided workflow; for example, to quantify the relative abundances of transcripts using ArrayStar. Note that this use case assumes the same reads are used for both rounds of assembly.

  1. Follow the steps described in RNA-Seq de novo transcriptome workflow. After assembly is complete, close the SeqMan NGen wizard.
  1. Launch SeqMan NGen.
  1. In the Choose Assembly Workflow screen, chose Transcriptome/RNA-Seq.
  1. In the Choose Assembly Type screen, choose Reference based assembly.
  1. In the Input Reference Sequences screen do one of the following:

    • Press Add Folder, navigate to the Transcriptome package that was output in Step 1, and press OK. Then choose which types of transcripts to input by checking one or both boxes at the bottom of the screen.

    • If you exported a subset of transcripts from SeqMan Pro and wish to use those, rather than the full Transcriptome package, press Add and add a single .fas file.
  1. In the Input Sequence Files and Define Experiments or Individual Replicates screen, load the desired reads. These can be the same reads that were used as input in the original transcript annotation workflow.
  1. Set other options, as desired, and run the assembly.

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