|Description||Hands On Lab Exercises for Galaxy|
|Related-course materials||Galaxy introduction|
|Authors||Alexis Dereeper (email@example.com)|
|Last Modified Date||15/03/2018|
- Practice 1: Basics of Galaxy (by Galaxy team)
- Practice 2: How to import datasets
- Practice 3: Concrete application: from reads to SNPs
Practice 1 : Basics of Galaxy (by Galaxy team)
Practice1 will be performed in the Galaxy main -
Practice1 consists of following the "Galaxy 101" hands-on provided by Galaxy team
Practice 2 : How to import datasets
Practice2 will be performed in the Galaxy South Green.
- Connect to Galaxy South Green -
- Log in using FormationN@cirad.fr account
- Rename your history "test data upload"
Test the different ways to import datasets into your history:
- Copy/paste the content of a dataset
- Copy/paste the link/URL of an external file to be imported -
- Upload any txt file from your local computer
- Use FTP procedure to upload big file following the procedure described form Galaxy homepage
- Import a dataset from a shared data library
Practice 3 : Concrete application: From reads to SNPs
Practice3 will be performed in the Galaxy South Green.
- Create a new history for this practice (ex: SNP calling)
Shared data => Data libraries, import into your history fastq datasets for 3 individuals (RC1, RC2, RC3) as well as reference fasta
Galaxy_trainings_2015 => NGS
- Check these 6 files and create a collection of 3 dataset pairs
Build a list of dataset pairs. Associate files by pair and give a name to your collection
- Process a FastqC analysis for RC1 to control the quality of sequencing
- Import the shared workflow called
- Observe the different steps of the workflow
- Run the complete workflow. It provides a collection of Bam files.
- Observe the final VCF output
The resource material is licensed under the Creative Commons Attribution 4.0 International License (here).