6
$\begingroup$

So I'm basically so new to this that I'm just trying to find out what tools, methods, and keywords I should go look up by myself.

I have a unique strain of a bacteria.

I was given RNAseq data for this unique strain.

I want to analyze the RNAseq data, but I need an annotated genome to do that.

As a resource, I do have the annotated genome of the common lab strain.

The common strain should be pretty similar to the unique strain, but I don't know how similar.

Can anyone tell me what tools/methods might be applicable so I can go look them up?

$\endgroup$
4
$\begingroup$

For a quick (but reliable) analysis, I'd recommend using Kallisto or Salmon to quantify isoform read counts using the transcriptome of the lab strain.

If you have a concern about transcripts that are in your sample but not in the lab strain, you can do two Trinity assemblies: one fully de-novo, and one genome-guided. These transcripts can then be used as a reference assembly for Kallisto/Salmon, and counts compared to the lab-strain results. Note that the Trinity assemblies will only apply to the particular environments that are in your samples; if a transcript isn't expressed, it won't be in the assembly.

Any transcripts in the de-novo assembly that are not in the genome-guided assembly are potentially novel to your strain. However, care must be taken in interpreting this: if there is any other contamination in the sample, those contaminant transcripts will also be assembled.

I'm not too familiar with annotation pipelines, but based on a couple of Twitter posts it looks like Prokka might be a reasonable start. Torsten Seeman (lead developer of Prokka) has done a post about alternative annotation pipelines:

http://thegenomefactory.blogspot.co.nz/2013/03/bacterial-genome-annotation-systems.html

$\endgroup$
2
  • 1
    $\begingroup$ bacterial person here: I can confirm that prokka is the de-facto standard annotation pipeline for bacterial genomes, and should do a great job in annotating all gene features $\endgroup$
    – mgalardini
    Sep 18 '17 at 7:41
  • 1
    $\begingroup$ Fantastic! Thank you so much for the great and detailed post, gringer! That helps so much! And thanks also mgalardini for confirming the info given! $\endgroup$
    – myflow
    Sep 18 '17 at 7:48

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.