Practical Section 0: Create a Galaxy account and get the data
In this course, we will analyze RNA sequencing data using public data on a web platform called Galaxy Project. This platform is open to the scientific community and is dedicated to intensive data analysis. Thanks to its graphical interphase, it helps scientists without coding background to perform bioinformatics analysis. To create an account in Galaxy, just follow the instructions:
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Go to https://usegalaxy.org/
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Click on “Login or Register”
- Click on “Register Here”
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Complete the registration form and click on "Create"
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ATTENTION, to use your Galaxy account you have to confirm your registration by clicking the link you will receive in your email box!
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Once this is done, we are ready to work!
We will perform the analysis using one of our public data sets which I have already uploaded to Galaxy. You will have to import the files to your Galaxy history following the instructions below.
The ZDDM Laboratory produced these data at GIGA-Ulg and it is part of the study "Pancreatic and intestinal endocrine cells in zebrafish share common transcriptomic signatures and regulatory programmes" (doi.org/10.1186/s12915-020-00840-1). In particular, we will use a subset of sequences to allow the analysis to run fast.
- The data is structured as followed:
- Two conditions: Wild type and Pax6 Mut pancreatic cells (WT and MUT)
- Each condition has 3 biological replicates
- The sequencing is Paired-end, then we will have two files by replicate corresponding to the reads forward (R1) and the reads reverse (R2)
- So, we will have 12 files (2 conditions x 3 replicates x 2 files by replicate)
- To get the data, you have to go to the main page of Galaxy and click the option "Upload Data" (first option) on the tools menu located on the left side of the screen.
- You will get the uploading menu (see picture below), you have to click the button Paste/Fetch data in which we will copy the following links. Make sure that you have selected the regular tab.
- Now, we will upload the data using the links below. In order to get the files organized and easy to find for the next steps, you need to copy the link and write the file name. Press again Paste/Fetch data to add the next file. Once you have added the 12 files, click on the button Start to initiate the uploading.
WT1_R1 https://usegalaxy.org/datasets/bbd44e69cb8906b59b48b4f8acc1afe6/display?to_ext=fastqsanger
WT1_R2 https://usegalaxy.org/datasets/bbd44e69cb8906b56ffd26f53292268a/display?to_ext=fastqsanger
WT2_R1 https://usegalaxy.org/datasets/bbd44e69cb8906b5dc135cfdc48d8089/display?to_ext=fastqsanger
WT2_R2 https://usegalaxy.org/datasets/bbd44e69cb8906b56a8d627c4f6b68ab/display?to_ext=fastqsanger
WT3_R1 https://usegalaxy.org/datasets/bbd44e69cb8906b581858f854fe86cd5/display?to_ext=fastqsanger
WT3_R2 https://usegalaxy.org/datasets/bbd44e69cb8906b58fb3d9efb1be923e/display?to_ext=fastqsanger
MUT1_R1 https://usegalaxy.org/datasets/bbd44e69cb8906b5f83d87abc4a3b84c/display?to_ext=fastqsanger
MUT1_R2 https://usegalaxy.org/datasets/bbd44e69cb8906b5a5f986baf67ac388/display?to_ext=fastqsanger
MUT2_R1 https://usegalaxy.org/datasets/bbd44e69cb8906b5ff7f3c6c38ed670d/display?to_ext=fastqsanger
MUT2_R2 https://usegalaxy.org/datasets/bbd44e69cb8906b56c392c8d8434b417/display?to_ext=fastqsanger
MUT3_R1 https://usegalaxy.org/datasets/bbd44e69cb8906b59e7978168e44e2af/display?to_ext=fastqsanger
MUT3_R2 https://usegalaxy.org/datasets/bbd44e69cb8906b53ac2bb3768dccef1/display?to_ext=fastqsanger
Additionally, we will upload two files that we will use on the next sections:
Zebrafish_Genome https://usegalaxy.org/datasets/bbd44e69cb8906b5176d6ddf4983730f/display?to_ext=fasta
Zebrafish_Annotation https://usegalaxy.org/datasets/bbd44e69cb8906b5cf0d676e02c3abfa/display?to_ext=gtf
Zebrafish_Annotation_bed https://usegalaxy.org/datasets/bbd44e69cb8906b5e26bf9236db9796c/display?to_ext=bed
4. Once the uploading is complete, you will see the files on your history (right side of the screen) in green color.
- Finally, there are 3 icons on each item of your history that will allow you to visualize, modify and remove the Data or result. Additionally, if you click on the name of your Data or result it will display the most important information about it.
- Now, we are ready to continue with the next section! 🤓