Difference between revisions of "Galaxy - Bioinformatics"
| (7 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| − | This page describes the use of [https://usegalaxy.org/ Galaxy] to analyze 16s rRNA HiSeq sequencing data. | + | 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. | + | 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). | + | 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): |
| + | :[[File:Screenshot 2023-05-25 at 12.19.03 PM.png|thumb|none]] | ||
| − | + | 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. | |
| − | |||
| − | The | + | ====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... | |
| − | |||
| − | |||
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):
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...