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Introduction to Genomics and Galaxy: Genomic interval tool search part corrected #4727

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Feb 15, 2024
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Introduction to Genomics and Galaxy: Genomic interval tool search part corrected #4727

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Genomic interval tool search part corrected - Update tutorial.md
sebastian-schaaf Feb 14, 2024
0bab813
Removed probably useless statement on sections button - Update tutori…
sebastian-schaaf Feb 15, 2024
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6 changes: 3 additions & 3 deletions topics/introduction/tutorials/galaxy-intro-strands/tutorial.md
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additionally, could anyone explain the part in brackets, in line 410?

"click the Show sections button (available on Galaxy servers)"

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I cannot. that looks like it could be removed.

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Ok, I removed the bracket, assuming noone will miss it...

Original file line number Diff line number Diff line change
Expand Up @@ -407,15 +407,15 @@ Galaxy excels at answering questions about genomic intervals and different sets

> <hands-on-title>Genomic Interval Tools</hands-on-title>
>
> * The next step is finding overlapping intervals, so type `interval` in the tool search box. There are many results from this search, so you might want to click the *Show sections* button (available on Galaxy servers) to see which sections the tools are organised into.
> * The next step is finding overlapping intervals, so type `interval` in the tool search box. There are many results from this search, so you might want to click the *Show sections* button to see which sections the tools are organised into.
> * *Explore* the tools in this toolbox, looking for something that we can use to see which genes on opposite strands overlap.
{: .hands_on}

Of the tools in the **Operate on Genomic Intervals** toolbox, **Join** and particularly **Intersect** have the most promise. Let's try **Intersect**.
Although there are the bedtools (section **BED**) and a section **Operate on Genomic Intervals** offering promising tools, the simple **Intersect** tool under **Text Manipulation** appears sufficient. Let's try **Intersect**.

> <hands-on-title>Genomic Interval Tools</hands-on-title>
>
> 1. {% tool [Intersect](toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/0.0.1) %} with the following parameters:
> 1. {% tool [Intersect](toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0) %} with the following parameters:
> - *"Return"*: `Overlapping Intervals`.
> This looks like it might return whole genes, while `Overlapping pieces` may return only the parts that overlap. We suspect that whole genes might be more useful.
> - {% icon param-files %}*"of"*: `Genes, forward strand` (the first dataset)
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