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Short read data

How to get short-read FASTQ files into Galaxy?

  • In the tool panel, click on Get Data
  • Click on EBI SRA. This will open the ENA webpage.
  • In the top right, next to the search bar, click on Advanced
  • For Select domain click Read
  • Select other options as required.

  • For example:
    • For Taxonomy and related enter Mycoplasma synoviae.

  • In the bottom right corner click Search

  • Click on Study
  • Click PRJNA183042
  • In the column FASTQ files (Galaxy) click on File 1
  • Galaxy will open in a new tab and this file will start to upload to your current history.
  • Go back to the EBI browser tab and click on File 2. This will also upload into your current history.
  • You can then close any open EBI browser tabs and any extra Galaxy tabs - you only need the one Galaxy tab open.

  • To repeat for other short read data, select Read and then choose options required, such as taxon, library layout, instrument type, or date created.