RNA-Seq de novo transcriptome workflow

With other applications, de novo assembly of RNA-Seq data can potentially result in thousands of unlabeled contigs representing the expressed transcripts. By contrast, SeqMan NGen automatically attempts to group contigs from the same gene, and then names and annotates them based on the best match to a collection of annotated reference sequences (the “Transcript Annotation Database”) extracted from data on NCBI’s RefSeq website. Results from this workflow are non-quantitative.

In this tutorial, you will de novo assemble an abbreviated set of paired end RNA-Seq sequences from Saccharomyces cerevisiae (yeast) from Nookaew I et al., 2012 and then examine the results. This workflow uses an abbreviated yeast data set with about 1 million reads per file.

The workflow is in two parts, which should be done in order:

• Part A: Setting up the transcriptome assembly in SeqMan NGen

• Part B: Viewing annotated transcripts in SeqMan Ultra