Therefore these tools are focused on improving existing annotations for non-model eukaryotic species, updating an annotation based on RNA-Seq data and/or generating transcript and gene tracks to serve as a common reference for differential expression analysis using the RNA-Seq Analysis tool.
The detection of novel transcripts from short-read sequencing data is only possible with low precision and sensitivity. Note that the Transcript Discovery tool has been tested to work well with other alignment tools including STAR, TopHat2, GSNAP and HISAT2. The Transcript Discovery plugin is designed to discover transcripts by mapping RNA-Seq sequencing reads to a genomic reference, allowing large gaps (for introns), followed by a transcript discovery process where transcripts are inferred from the read mappings.
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