Assessing Rockhopper's output

Question

[langziv]

Hi.
The output includes transcripts that are hundreds of bases long, but also some that are thousands of bases long, which I'm not sure is what's expected on a transcriptome.
I'd love to get some opinions on how to assess a de novo transcriptome from your experience and knowledge, and also on possible ways to improve results by passing/setting certain parameters when running Rockhopper.
Thanks!

Answer 1

[shelkmike]

I didn't do de novo transcriptome assemblies with Rockhopper. Only reference-based analyses. However, having very long transcripts is normal for bacteria, because bacterial operons often contain many genes.

[langziv]

Thanks.
Did you get to use an assembly, rather than a genome, as a reference?

[shelkmike]

I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.

[langziv]

I see.
I tried using the GUI Rockhopper for RNA-seq analysis of a K. pneumoniae strain, but the program didn't find the strain's assembly (there's no genome for this strain). when I tried using the command-line Rockhopper with the assembly, it resulted in an error. That made me think that the program works only with genomes as references.
Therefore, I was able to use the program only with a de novo assembled transcriptome.