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Other options

Out of date

Please see the updated version of this tutorial.

There are some other optional things you can pass to JBrowse Linear View when you create it

location​

This is the location you would like the view to be in when it opens. For example, if you wanted to have the view open to chromosome 1 from position 100,987,269 to position 100,987,368, you could specify it in one of these ways:

  • 1:100987269..100987368
  • 1:100987269-100987368
  • 1:100,987,269..100,987,368
  • chr1:100987269..100987368 (if you have aliases set up)

plugins​

JBrowse 2 allows you to provide plugins to add new features or modify behavior. We won't get into them today, but you can read more about creating a plugin here.

defaultSession​

The "session" is the state of the view, e.g. what location is visible, what tracks are open, whether the overview bar is open, etc. We'll get into this more later in the tutorial.

onChange​

This is a function you can provide that runs each time something in the view changes. We'll also talk about this more later in the tutorial.

configuration​

This is a place to put top-level configuration. It's mostly reserved for future use, so you won't need to worry about it right now.