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Assessing Rockhopper's output

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!

transcriptome rockhopper rna-seq de-novo-assembly
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written by langziv • langziv

1 answer

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.

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written by shelkmike shelkmike

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

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written by langziv • langziv

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

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written by shelkmike shelkmike

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.

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written by langziv • langziv

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