A short introduction to Galaxy

Overview

Questions
  • How to get started in Galaxy
Objectives
  • Learn how to upload a file
  • Learn how to use a tool
  • Learn how to view results
  • Learn how to view histories

Time estimation: 30 minutes

Overview

Agenda

  1. What does Galaxy look like?
  2. Key Galaxy actions
    1. Name your current history
    2. Upload a file
    3. Use a tool
    4. View results
    5. Run another tool
    6. Re-run that tool with changed settings
    7. Create a new history
    8. Look at all your histories

What does Galaxy look like?

Hands-on: Log in to Galaxy

  1. Open your favorite browser (Chrome, Safari or Firefox as your browser, not Internet Explorer!)
  2. Browse to your Galaxy instance
  3. Log in or register

login

Different Galaxy servers

This is an image of Galaxy Australia, located at usegalaxy.org.au

The particular Galaxy server that you are using may look slightly different and have a different web address:

You can also find more possible Galaxy servers at the top of this tutorial in Galaxy instances

The Galaxy homepage is divided into three panels:

galaxy overview screenshot

The first time you use Galaxy, there will be no files in your history panel.

Key Galaxy actions

Name your current history

Your “History” is in the panel at the right.

Hands-on: Name history

  1. Go to the History panel (on the right)

  2. Click on the history name (which by default is “Unnamed history”)

    name history

  3. Type in a new name, for example, “My-Analysis”
  4. Press Enter on your keyboard to save it

Upload a file

Your “Tools” are in the panel at the left.

Hands-on: Upload a file from URL

  1. Go to the Tools panel (on the left)
  2. Click Get Data (at the top of the list)

  3. Click Upload File

    This brings up a box:

    filebox

  4. Click Paste/Fetch data

  5. Paste in the address of a file:

    https://zenodo.org/record/582600/files/mutant_R1.fastq
  6. Click Start
  7. Click Close

Your uploaded file is now in your current history. When the file has uploaded to Galaxy, it will turn green.

Comment

After this you will see your first history item in Galaxy’s right panel. It will go through the gray (preparing/queued) and yellow (running) states to become green (success).

What is this file?

Hands-on: View the file content

  1. Click on the (eye) icon next to the file name, to look at the file content

    eye

The contents of the file will be displayed in the central Galaxy panel.

This file contains DNA sequencing reads from a bacteria, in FASTQ format:

fastq

Use a tool

Let’s look at the quality of the reads in this file.

Hands-on: Use a tool

  1. Type FastQC in the tools panel search box (top)

  2. Click on the FastQC tool

    The tool will be displayed in the central Galaxy panel.

  3. Select the following parameters:
    • “Short read data from your current history”: the FASTQ file that we uploaded
    • No change in the other parameters
  4. Click Execute

This tool will run and the two output files will appear at the top of your history panel.

View results

We will look at the output file called FastQC on data 1: Webpage.

Comment

  • Note that Galaxy has given this file a name according to both the tool name (“FastQC”) and the dataset (“data 1”) that it used.
  • The name “data 1” means the dataset number 1 in Galaxy’s current history (our FASTQ file).

Hands-on: View results

  • Click on the (eye) icon next to the output file.

    The information is displayed in the central panel

    fastqc-out

This tool has summarised information about all of the reads in our FASTQ file.

Questions

  1. What was the length of the reads in the input FASTQ file?
  2. Do these reads have higher quality scores in the centre or at the ends?

Solutions

  1. 150 bp
  2. In the center

Run another tool

Let’s run a tool to filter out lower-quality reads from our FASTQ file.

Hands-on: Run another tool

  1. Type Filter by quality
  2. Click on the tool Filter by quality
  3. Set the following parameters:
    • “Library to filter”: the input FASTQ file
    • “Quality cut-off value”: 35
    • “Percent of bases in sequence that must have quality equal to / higher than cut-off value”: 80
  4. Click Execute

After the tool has run, the output file will appear at the top of your History panel.

What are the results from this filtering tool?

We could click on the eye icon to view the contents of this output file, but it will not be very informative - we will just see a list of reads.

Hands-on: Get metadata about a file

  1. Click on the output file name in the History panel

    This expands the information about the file.

    filter1

Questions

How many read has been discarded

Solutions

1786 low-quality reads were discarded

Re-run that tool with changed settings

We have now decided that our input reads have to be filtered to an even higher standard. We will change the filter settings and re-run the tool.

Hands-on: Re-run the tool

  1. Click on the icon (Run this job again) for the output dataset of Filter by quality

    rerun

    This brings up the tool interface in the central panel with the parameters set to the values used previously to generate this dataset.

  2. Change the settings to something even stricter

    For example, you might decide you want 80 percent of bases to have a quality of 36 or higher, instead of 35.

  3. Click Execute
  4. View the results: Click on the output file name to expand the information. (Note: not the (eye) icon.)

Questions

How many reads were discarded under these new filtering conditions?

You can re-run a tool many times with different settings. Each time you re-run the tool, the new output file will appear at the top of your current history.

Create a new history

Let’s create a new history.

Hands-on: New history

  1. Click on the (gear) icon (History options) in the History panel

    cog

  2. Select Create New
  3. Name your history, e.g. “Next-analysis”
  4. Press Enter

This new history does not have any files in it yet.

Look at all your histories

Where is your first history, called “my-analysis”?

Hands-on: View histories

  1. Click on the View all histories ( icon) at the top right of your history

    view-hist

    A new page will appear with all your histories displayed here.

  2. Copy a dataset into your new history
    1. Click on the FASTQ file in “my-analysis” history
    2. Drag it into the “Next-analysis” history

    This makes a copy of the dataset in the new history (without actually using additional disk space).

  3. Click on Analyze Data in the top panel to go back to your analysis window

view-all-hist

Your main Galaxy window will now show the current history as “Next-analysis”, and it will have one dataset in it.

At any time, you can go back into the “View all histories” page and “Switch to” a different history.

Conclusion

Well done! You have completed the short introduction to Galaxy, where you named the history, uploaded a file, used a tool, and viewed results. Additional tutorials are available for a more in-depth introduction to Galaxy’s features.

Key points

  • The Galaxy interface has tools on the left, viewing pane in the middle, and a history of your data analysis on the right.
  • You can create a new history for each analysis. All your histories are saved.
  • To get data into Galaxy, you can upload a file by pasting in a web address. There are other ways to get data into Galaxy (not covered in this tutorial): you can upload a file from your computer, and you can import an entire history.
  • Choose a tool and change any settings for your analysis.
  • Run the tool. The output files will be saved at the top of your history.
  • View the output files by clicking on the eye icon.
  • View all your histories and move files between them. Switch to a different history.
  • Log out of your Galaxy server. When you log back in (to the same server), your histories will all be there.

Congratulations on successfully completing this tutorial!