Relying heavily on reads mapped with a gap as evidence for transcripts, the plugin is primarily developed for eukaryotic genomes. The proposed workflow for using the ab initio Transcript Discovery plugin in combination with the existing RNA-seq tool in CLC Genomics Workbench is this:
If you have sequenced several samples that need to be compared, we suggest using the reads from all samples for the large gap mapping and subsequent transcript discovery. This way, you can establish a common set of reference transcripts and genes that makes it possible to compare gene expression levels across samples (using the RNA-seq tool in CLC Genomics Workbench). The initial read mapping created by the large gap mapper is then no longer used and can be deleted, unless you wish to be able to go back and double-check the basis of the prediction.
The current release is a beta version with full functionality for single reads. If you have paired reads, these are treated as single reads. However, when you run subsequent RNA-seq analysis to quantify expression across genes and transcripts, the full paired information is used.