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. This workflow uses an abbreviated yeast data set with about 1 million reads per file.

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 name and annotate 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.

Begin with Part A: Setting up and running an RNA-Seq de novo transcriptome assembly in SeqMan NGen.

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