Answers.Body: <p>For a quick (but reliable) analysis, I'd recommend using <a href="https://pachterlab.github.io/kallisto/download" rel="nofollow noreferrer">Kallisto</a> or <a href="https://github.com/COMBINE-lab/salmon/releases" rel="nofollow noreferrer">Salmon</a> to quantify isoform read counts using the transcriptome of the lab strain.</p>
  <p>If you have a concern about transcripts that are in your sample but not in the lab strain, you can do two <a href="https://github.com/trinityrnaseq/trinityrnaseq/releases" rel="nofollow noreferrer">Trinity</a> assemblies: one fully <em>de-novo</em>, and one <a href="https://github.com/trinityrnaseq/trinityrnaseq/wiki/Genome-Guided-Trinity-Transcriptome-Assembly" rel="nofollow noreferrer">genome-guided</a>. 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.</p>
  <p>Any transcripts in the <em>de-novo</em> 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.</p>
  <p>I'm not too familiar with annotation pipelines, but based on a couple of Twitter posts it looks like <a href="http://www.vicbioinformatics.com/software.prokka.shtml" rel="nofollow noreferrer">Prokka</a> might be a reasonable start. Torsten Seeman (lead developer of Prokka) has done a post about alternative annotation pipelines:</p>
  <p><a href="http://thegenomefactory.blogspot.co.nz/2013/03/bacterial-genome-annotation-systems.html" rel="nofollow noreferrer">http://thegenomefactory.blogspot.co.nz/2013/03/bacterial-genome-annotation-systems.html</a></p>
  <p>Update: Torsten Seeman <a href="https://twitter.com/torstenseemann/status/1565471892840259585" rel="nofollow noreferrer">now recommends</a> Bakta as a &quot;worthy successor to Prokka&quot;:</p>
  <p><a href="https://github.com/oschwengers/bakta" rel="nofollow noreferrer">https://github.com/oschwengers/bakta</a></p>
  <blockquote>
  <p>Bakta is a tool for the rapid &amp; standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. It provides dbxref-rich, sORF-including and taxon-independent annotations in machine-readable JSON &amp; bioinformatics standard file formats for automated downstream analysis.</p>
  </blockquote>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-09-18T07:41:48.460Z
Answers.Text: 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
Answers.UserDisplayName: mgalardini
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-09-18T07:48:24.917Z
Answers.Text: 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!
Answers.UserDisplayName: myflow
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Answers.LastEditDate: 2023-12-22T08:14:13.557Z
Answers.UserDisplayName: gringer
Body: <p>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.</p>
  
  <p>I have a unique strain of a bacteria.</p>
  
  <p>I was given RNAseq data for this unique strain.</p>
  
  <p>I want to analyze the RNAseq data, but I need an annotated genome to do that.</p>
  
  <p>As a resource, I do have the annotated genome of the common lab strain.</p>
  
  <p>The common strain should be pretty similar to the unique strain, but I don't know how similar.</p>
  
  <p>Can anyone tell me what tools/methods might be applicable so I can go look them up?</p>
  
Tags: <rna-seq><sequence-annotation><reference-genome>
Title: Bacterial genome annotation of a clinical isolate strain?
ThreadText: # Bacterial genome annotation of a clinical isolate strain?
  
  (Asked by: username_0 on 2017-09-17)
  
  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?
  
  **Tags:** rna-seq, sequence-annotation, reference-genome
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-09-18. Score: 5 | Accepted answer
  
  For a quick (but reliable) analysis, I'd recommend using [Kallisto](https://pachterlab.github.io/kallisto/download) or [Salmon](https://github.com/COMBINE-lab/salmon/releases) 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](https://github.com/trinityrnaseq/trinityrnaseq/releases) assemblies: one fully *de-novo*, and one [genome-guided](https://github.com/trinityrnaseq/trinityrnaseq/wiki/Genome-Guided-Trinity-Transcriptome-Assembly). 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](http://www.vicbioinformatics.com/software.prokka.shtml) 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>
  
  Update: Torsten Seeman [now recommends](https://twitter.com/torstenseemann/status/1565471892840259585) Bakta as a "worthy successor to Prokka":
  
  <https://github.com/oschwengers/bakta>
  
  > Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. It provides dbxref-rich, sORF-including and taxon-independent annotations in machine-readable JSON & bioinformatics standard file formats for automated downstream analysis.
  
  > **Comments:**
  > **username_2**: 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  
  > **username_0**: Fantastic! Thank you so much for the great and detailed post, username_1! That helps so much! And thanks also username_2 for confirming the info given!  
  
  ---
  
  