Frequently Asked Questions

Rule-builder

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

Tip: 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”: BThis 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 Execute

The tool will execute and reshape your list, congratulations!


Visualisation

Using IGV with Galaxy

Tip: 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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