Use RNA-Seq de novo transcriptome output as a reference

You may use the contigs output from an RNA-seq de novo workflow as reference sequences in the templated RNA-Seq workflow. Doing this may allow you 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 RNA-Seq de novo transcriptome workflow. After assembly is complete, close the SeqMan NGen wizard.

2. Launch SeqMan NGen again and follow the RNA-seq templated workflow.

3. In the Reference Sequence 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 Ultra and wish to use those, rather than the full Transcriptome package, press Add and add a single .fas file.

*Note: SeqMan NGen does not support the addition of more than one .fas file from the .Transcriptome folder.

4. In the Input Sequences, load the desired reads. These can be the same reads that were used as input in the original transcript annotation workflow.

5. Set other options, as desired, and run the assembly.