Frequently Asked Questions

Rule-builder

Flatten a list of list of paired datasets into a list of paired datasets

Sometimes you find yourself with a list:list:paired, i.e. a collection of collection of paired end data, and you really want a list:paired, a flatter collection of paired end data. This is easy to resolve with Apply rules:

  1. Open Apply rules
  2. Select your collection
  3. Click Edit

You’ll now be in the Apply rules editing interface. There are three columns (if it’s a list:list:paired)

  1. The outermost list identifier(s)
  2. The next list identifier(s)
  3. The paired-end indicator

Flattening this top level list, so it’s just a list:paired requires a few changes:

  1. From Column menu select Concatenate Columns
    • “From Column”: A
    • “From Column”: B This creates a column with the top list identifier, and the inner list identifier, which will be our new list identifier for the flattened list.
  2. From Rules menu select Add / Modify Column Definitions
    • Click Add Definition button and select Paired-end Indicator
      • “Paired-end Indicator”: C
    • Click Add Definition button and select List Identifier(s)
      • “List Identifier(s)”: D
    • Click Apply
  3. Click Save
  4. Click Run Tool

The tool will execute and reshape your list, congratulations!


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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