Difference between revisions of "Galaxy - Bioinformatics"

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This page describes the use of [https://usegalaxy.org/ Galaxy] to analyze 16s rRNA HiSeq sequencing data.
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This page describes the use of [https://usegalaxy.org/ Galaxy] to analyze 16s rRNA HiSeq sequencing data. Although ''usegalaxy.org'' is a free resource from MIT, it is also possible to install this software on your own server. At this time, the following content will ass-u-me that we are using the main usegalaxy.org site.
  
 
===Setting up Account===
 
===Setting up Account===
It is recommended that you setup a free account with Galaxy so that you can save your work.
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It is recommended that you setup a free account with Galaxy so that you can save your work. Some feature will give false error messages if not logged in to an account, since free user you are given a certain amount of storage space. '''''NOTE: You will be sent an email that contains a link to verify your email address associated with the account before beginning; errors will occur if not verified/logged in.'''''
  
 
===Galaxy Training Network (GTN)===
 
===Galaxy Training Network (GTN)===
There is a [https://training.galaxyproject.org/ Galaxy training site] that is very useful called GTN (Galaxy Training Network). In particular, this page is interested in the tutorial under [https://training.galaxyproject.org/training-material/topics/metagenomics/ Metagenomics]...and specifically the tutorial labeled:
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There is a [https://training.galaxyproject.org/ Galaxy training site] that is very useful called GTN (Galaxy Training Network). This site was recently added to the [https://usegalaxy.org/ Galaxy] Toolbar (graduation cap):
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:[[File:Screenshot 2023-05-25 at 12.19.03 PM.png|thumb|none]]
  
: -''16S Microbial Analysis with mothur (extended)'' or
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This built-in tutorial feature allows you to shift easily between the tutorial and the Galaxy interface, as well as allows direct click-access to the tools and workflow.
:- ''16S Microbial Analysis with mothur (short)''
 
  
The difference between extended and short will be realized once you become familiar with the processing, but for now it is best to use the ''short'' version since it uses "workflows" (multi-step processing) as opposed to executing each step individually. You might be tempted to use the ''extended'' version so that you will understand all parts, but for now i strongly recommend the ''short'' version.
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====Your first Galaxy Training====
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The first recommended tutorial analyzes the gut bacteria of age-dependent mice. The tutorial will show how to download the data and generate a taxonomic classification...and more!
  
====GTN Tutorial Video====
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To get started (recommended)...
There is a video that will walk you thru the 16s tutorial using the ''short'' version above:
 
:- [https://youtu.be/CGSBeCW3rpA Newest version, May 2023] <--available through a link on the GTN - 16S Microbial Analysis with mothur (short) under "Recordings."
 
:- [https://www.youtube.com/watch?v=mto4Nl-q7Kk a previous recording, March 2021]
 
  
====Data====
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:1. Launch and login to Galaxy.
The tutorial above uses a set of data described in the introduction. If you wish to follow the tutorial using some Monmouth College Data, you can download the 2 files below:
 
:-
 
  
====Processing Steps====
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:2. click the GTN icon (graduation cap) in the toolbar,
<gallery>
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File:Screenshot 2023-05-22 at 8.18.42 AM.png
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:3. scroll down and select the ''Metagenomics'' link, then to the ''16S Microbial Analysis with mothur (short).'' NOTE: there is a recorded YouTube video (see Recordings link after the name) that walks you thru the tutorial. I suggest you launch this tutorial on a second computer/projector/TV in 360 and then follow the tutorial on your laptop.
File:Screenshot 2023-05-25 at 10.54.11 AM.png
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File:Screenshot 2023-05-25 at 10.54.26 AM.png
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:4 Follow the video tutorial instructions...
File:Screenshot 2023-05-25 at 10.54.37 AM.png
 
</gallery>
 
[[File:Screenshot 2023-05-25 at 10.55.08 AM.png|thumb|none]]
 

Latest revision as of 17:29, 25 May 2023

This page describes the use of Galaxy to analyze 16s rRNA HiSeq sequencing data. Although usegalaxy.org is a free resource from MIT, it is also possible to install this software on your own server. At this time, the following content will ass-u-me that we are using the main usegalaxy.org site.

Setting up Account

It is recommended that you setup a free account with Galaxy so that you can save your work. Some feature will give false error messages if not logged in to an account, since free user you are given a certain amount of storage space. NOTE: You will be sent an email that contains a link to verify your email address associated with the account before beginning; errors will occur if not verified/logged in.

Galaxy Training Network (GTN)

There is a Galaxy training site that is very useful called GTN (Galaxy Training Network). This site was recently added to the Galaxy Toolbar (graduation cap):

Screenshot 2023-05-25 at 12.19.03 PM.png

This built-in tutorial feature allows you to shift easily between the tutorial and the Galaxy interface, as well as allows direct click-access to the tools and workflow.

Your first Galaxy Training

The first recommended tutorial analyzes the gut bacteria of age-dependent mice. The tutorial will show how to download the data and generate a taxonomic classification...and more!

To get started (recommended)...

1. Launch and login to Galaxy.
2. click the GTN icon (graduation cap) in the toolbar,
3. scroll down and select the Metagenomics link, then to the 16S Microbial Analysis with mothur (short). NOTE: there is a recorded YouTube video (see Recordings link after the name) that walks you thru the tutorial. I suggest you launch this tutorial on a second computer/projector/TV in 360 and then follow the tutorial on your laptop.
4 Follow the video tutorial instructions...