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Merge pull request #4727 from sebastian-schaaf/fix_strands_tutorial_a…
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Introduction to Genomics and Galaxy: Genomic interval tool search part corrected
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hexylena authored Feb 15, 2024
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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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