<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>

CC BY-SA 4.0
2022-02-18T16:33:30.263Z
2022-02-18T16:33:30.263Z
Kamil S Jaron
<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>

<phylogenetics><transcriptome><galaxy><kallisto>
use Kallisto in galaxy
# 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

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## 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.


---

