From ac9e636ebdb52a9067f1bec238287aa88a9e4226 Mon Sep 17 00:00:00 2001 From: sebastian-schaaf <128363933+sebastian-schaaf@users.noreply.github.com> Date: Wed, 14 Feb 2024 10:50:45 +0100 Subject: [PATCH 1/2] Genomic interval tool search part corrected - Update tutorial.md Addressing https://github.com/galaxyproject/training-material/issues/4174 in biref: The 'Intersect' keyword motivated to type to the search box did not give literal tool result in section "Operate on Genomic Intervals toolbox, Join and particularly Intersect" anymore. --- .../introduction/tutorials/galaxy-intro-strands/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/introduction/tutorials/galaxy-intro-strands/tutorial.md b/topics/introduction/tutorials/galaxy-intro-strands/tutorial.md index 566aa541845d49..6d76816646bda4 100644 --- a/topics/introduction/tutorials/galaxy-intro-strands/tutorial.md +++ b/topics/introduction/tutorials/galaxy-intro-strands/tutorial.md @@ -411,11 +411,11 @@ Galaxy excels at answering questions about genomic intervals and different sets > * *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**. > Genomic Interval Tools > -> 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) From 0bab813dee9845673e49cee4d6ae9b69119110d7 Mon Sep 17 00:00:00 2001 From: sebastian-schaaf <128363933+sebastian-schaaf@users.noreply.github.com> Date: Thu, 15 Feb 2024 09:22:47 +0100 Subject: [PATCH 2/2] Removed probably useless statement on sections button - Update tutorial.md Agree with @hexylena https://github.com/galaxyproject/training-material/pull/4727#discussion_r1490557747 --- topics/introduction/tutorials/galaxy-intro-strands/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/introduction/tutorials/galaxy-intro-strands/tutorial.md b/topics/introduction/tutorials/galaxy-intro-strands/tutorial.md index 6d76816646bda4..3e47a527211624 100644 --- a/topics/introduction/tutorials/galaxy-intro-strands/tutorial.md +++ b/topics/introduction/tutorials/galaxy-intro-strands/tutorial.md @@ -407,7 +407,7 @@ Galaxy excels at answering questions about genomic intervals and different sets > Genomic Interval Tools > -> * 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}