The templated Transcriptome/RNA-Seq 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.
In this workflow, first-pass assembly is done using the usual XNG assembler. Second-pass assembly utilizes the QNG analysis module—based on an algorithm used in ArrayStar with QSeq—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
After performing a templated Transcriptome/RNA-Seq assembly, you can launch the assembly in SeqMan Pro to view this information in the Feature Table, which consists of three tabs:
•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.
Alternatively, you may wish to view the assembly in DNASTAR’s GenVision Pro, where you can elect to display a Sashimi plot for the assembly. Sashimi plots are designed to display data indicative of mRNA splicing. All necessary Sashimi data are generated automatically during RNA-Seq assembly.
See the topic Reference-Based Transcriptome/RNA-Seq Workflow Output for a list of output files resulting from this type of assembly.
See Using Transcript Annotation (StarBlast) Workflow Output as the Template to learn how to use the output of a de novo transcriptome/RNA-Seq assembly as input for the templated transcriptome/RNA-Seq workflow.