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:
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:
|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.|
Need more help with this?