Did you arrive here by selecting the   DNASTAR Navigator workflow Transcriptomics > RNA-seq? If so, you’re in the right place!      

The RNA-Seq reference-guided workflow is specified by choosing Transcriptome/RNA-Seq in the Choose Assembly Workflow screen, and Templated assembly – normal workflows in the Choose Assembly Type screen.

The following brief video shows an overview of the workflow:

In this workflow, first-pass assembly is done using the usual XNG assembler. Second-pass assembly utilizes the QNG analysis module to determine expression level statistics.

For each sample in a project, two new files for each contig/chromosome are put into the .assembly package. These contain the QNG calculated expression values for each gene and its isoforms:

  • [sample name]-[contig number].genes-features.
  • [sample name]-[contig number].isoforms-features

If you wish, you can use the output of an RNA-Seq de novo transcriptome assembly as input for the RNA-Seq reference-guided workflow. To learn how to do this, see Use RNA-Seq de novo transcriptome output as a reference.

After performing an RNA-Seq reference-guided assembly, you can do any of the following:

Application Notes
SeqMan Pro Use SeqMan Pro’s 3-tabbed Feature Table for downstream analysis:

* All Features
* Gene Features
* CDS Features

Each tab displays expression values in a column entitled “RPKM”. If the sample is part of a replicate set, a second column entitled “RPKM – Replicate” displays the expression value for the feature determined from the replicate set.
GenVision Pro Display a Sashimi plot for the assembly. Sashimi plots are designed to display data indicative of mRNA splicing, and are generated automatically during RNA-Seq assembly. See RNA-Seq reference-guided workflow output for a list of output files resulting from this type of assembly.
ArrayStar Use ArrayStar’s Gene and Isoform tables to filter for differentially-expressed genes of interest. ArrayStar tables can also display any DESeq2 or edgeR statistics included in the assembly.

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