Frequently Asked Questions

Igv

Add Mapped reads track to IGV from Galaxy

  1. Install IGV (if not already installed)
  2. Launch IGV on your computer
  3. Check if the reference genome is available on the IGV instance
  4. Expand the BAM dataset with the mapped reads in the history
  5. Click on the local in display with IGV to load the reads into the IGV browser

  6. Switch to the IGV instance

    The mapped reads track should appear. Be sure that all files have the same genome ID

Add genome and annotations to IGV from Galaxy

  1. Upload a FASTA file with the reference genome and a GFF3 file with its annotation in the history (if not already there)
  2. Install IGV (if not already installed)
  3. Launch IGV on your computer
  4. Expand the FASTA dataset with the genome in the history
  5. Click on the local in display with IGV to load the genome into the IGV browser
  6. Wait until all Dataset status are ok

  7. Close the window

    An alert ERROR Parameter "file" is required may appear. Ignore it.

  8. Expand the GFF3 dataset with the annotations of the genome in the history
  9. Click on the local in display with IGV to load the annotation into the IGV browser

  10. Switch to the IGV instance

    The annotation track should appear. Be careful that all files have the same genome ID


Visualisation

Using IGV with Galaxy

You can send data from your Galaxy history to IGV for viewing as follows:

  1. Install IGV on your computer (IGV download page)
  2. Start IGV
  3. In recent versions of IGV, you will have to enable the port:
    • In IGV, go to View > Preferences > Advanced
    • Check the box Enable Port
  4. In Galaxy, expand the dataset you would like to view in IGV
    • Make sure you have set a reference genome/database correctly (dbkey) (instructions)
    • Under display in IGV, click on local


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