Using example data

Example data can be used to run this workflow. The original tutorial has provided some example data that can be easily downloaded from here and used in Galaxy. For this workflow, it’s better to use the subsetted example files to run this workflow. (Use the files that have the prefix subset_)

  • On the homepage of Galaxy, on the left-hand side, click on “Upload data”

  • Click on the “Paste/Fetch data” button on the textbox that appears

  • Paste the below lines and then click “Start”

https://zenodo.org/record/3457880/files/subset_pbmc_1k_v3_S1_L001_R1_001.fastq.gz
https://zenodo.org/record/3457880/files/subset_pbmc_1k_v3_S1_L001_R2_001.fastq.gz
https://zenodo.org/record/3457880/files/subset_pbmc_1k_v3_S1_L002_R1_001.fastq.gz
https://zenodo.org/record/3457880/files/subset_pbmc_1k_v3_S1_L002_R2_001.fastq.gz

  • The files should start uploading. One more way is to download the files to your computer from the site and upload them to Filezilla and use FTP to transfer these files. Instructions are here

  • You are now ready to use your fastq files. The next step so as to make it workflow ready is to create a collection of fastq files. Please refer to these instructions to create a collection of your files.