Answers.Body: <p>You have to click on the dropdown menu and select &quot;Use transcriptome from history&quot;, which will allow you to specify your own file.</p>
  <p><a href="https://i.sstatic.net/YysIr.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/YysIr.png" alt="enter image description here" /></a></p>
  <p>I suspect the default will be built-in human transcriptome.</p>
  <p>Solution is not tested, so let us know if it actually works.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-02-18T16:33:30.263Z
Answers.LastActivityDate: 2022-02-18T16:33:30.263Z
Answers.UserDisplayName: Kamil S Jaron
Body: <p>I want to use <a href="https://pachterlab.github.io/kallisto/about" rel="nofollow noreferrer">Kallisto</a> for sequence alignment in Galaxy. Its description is:</p>
  <blockquote>
  <p>a program for quantifying abundances of transcripts from bulk and
  single-cell RNA-Seq data, or more generally of target sequences using
  high-throughput sequencing reads.</p>
  </blockquote>
  <p>However, I found this field empty:</p>
  <blockquote>
  <p><strong>there is no option available for the reference transcriptome.</strong></p>
  </blockquote>
  <ul>
  <li>How I use a reference sequence?</li>
  <li>Can I leave the other configuration by default?</li>
  </ul>
  <ul>
  <li>this is the link of the tool:  <a href="https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3" rel="nofollow noreferrer">https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3</a></li>
  </ul>
  <p><a href="https://i.sstatic.net/Xn5I1.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/Xn5I1.png" alt="enter image description here" /></a></p>
  
Tags: <phylogenetics><transcriptome><galaxy><kallisto>
Title: use Kallisto in galaxy
ThreadText: # use Kallisto in galaxy
  
  (Asked by: username_0 on 2021-06-22)
  
  I want to use [Kallisto](https://pachterlab.github.io/kallisto/about) for sequence alignment in Galaxy. Its description is:
  
  > a program for quantifying abundances of transcripts from bulk and
  > single-cell RNA-Seq data, or more generally of target sequences using
  > high-throughput sequencing reads.
  
  However, I found this field empty:
  
  > **there is no option available for the reference transcriptome.**
  
  * How I use a reference sequence?
  * Can I leave the other configuration by default?
  
  * this is the link of the tool: <https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3>
  
  [![enter image description here](https://i.sstatic.net/Xn5I1.png)](https://i.sstatic.net/Xn5I1.png)
  
  **Tags:** phylogenetics, transcriptome, galaxy, kallisto
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-02-18. Score: 1
  
  You have to click on the dropdown menu and select "Use transcriptome from history", which will allow you to specify your own file.
  
  [![enter image description here](https://i.sstatic.net/YysIr.png)](https://i.sstatic.net/YysIr.png)
  
  I suspect the default will be built-in human transcriptome.
  
  Solution is not tested, so let us know if it actually works.
  
  
  ---
  
  