Graph Track Operators
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Get the graph track operations test file. There is probably a copy in the code base in the test sources in the Track Operations module.
You can just paste this into a text file, or download it from here: TrackOperationsTesting1.bedgraph
# genome_version = A_thaliana_Jun_2009
track type=bedgraph name="TrackOperationsTesting1" description="Even numbers" color=0,128,0
Chr1 0 245144 0
Chr1 245144 735432 2
Chr1 735432 1470864 4
Chr1 1470864 2206296 8
Chr1 2206296 3186872 16
Chr1 3186872 3922304 20
Chr1 3922304 4412592 14
Chr1 4412592 4657736 20
Chr1 4657736 5148024 10
Chr1 5148024 5393168 6
Chr1 5393168 5638312 6
Chr1 5638312 5883456 4
Chr2 0 245144 2
Chr2 245144 490288 2
Chr2 490288 735432 2
Chr2 735432 1225720 4
Chr2 1225720 1470864 4
Chr2 1470864 1716008 8
Chr2 1716008 2206296 8
Chr2 2206296 186872 16
Chr2 3186872 3922304 20
Chr2 3922304 4167448 14
Chr2 4167448 4412592 0
Chr2 4412592 4657736 20
Chr2 4657736 4902880 10
Chr2 4902880 5148024 10
Chr2 5148024 5393168 6
Chr2 5393168 5638312 0
Chr2 5638312 5883456 0
Add the track operations test file. You can do this without selecting any genome, just drag/drop the file onto the home screen. Change the Load Mode to Genome. In the Graph panel, under Options, select StairStep.
At any point in this process, if you get a graph that appears blank, or has a Y-axis with values like 249,999,999,999,999.97Y, adjust the max of the Y-axis scale to match the image here, or to something you know to be logical. This odd appearance comes up when the operation produces infinity (perhaps by taking the inverse of 0) and the track height is trying to accommodate that as the max value, which pushes all actual values down to an invisible size. If you do encounter this, make note of it wherever you are documenting the testing process.
Go to the Graph panel, and select the Even Numbers track.
Go to the Data Access panel and remove each of the tracks you created.
Go to the Graph panel, and select the Even Numbers track.
Go to the Data Access panel and remove each of the tracks you created. Return to the Graph panel, and select the Even Numbers track.
Go to the Graph panel, and select the Even Numbers track.
Select all three of these tracks; hold the shift key and click on each. With all three selected, do the following:
Select the Even Numbers track and the Inverse: Inverse: Even Numbers track.
Select all tracks and choose StairStep. Select the track called Diff Even Numbers, Inverse: Inverse: Even Numbers
Observe that:
Go to the Graph panel, and select the Even Numbers track.
Select the Even Numbers track,
Arrange the tracks so that the green track "Inverse Thing" is above the corresponding pink track "Inverse: Thing". Set all track to StairStep. See image.
For each pair, use the Milti-Graph operation Diff to create a new track. Make these new tracks blue, and StairStep. Like the Diff Inverse Inverse case above, these blue tracks should be all 0-values.
Verify that:
Go to the Selection Info panel and verify that all tracks have the expected y coord corresponding to the original value of 16:
Go to the Data Access panel and remove each of the tracks you created Except: "Inverse: Log3", and "Inverse: Natural Log" . Return to the Graph panel, and select the Even Numbers track.
Add the track operations test file. You can do this without selecting any genome, just drag/drop the file onto the home screen. Change the Load Mode to Genome.
Make the Odd Numbers track:
Remove the track with the yellow highlight. The two TrackOperationsTest files are what you will use to test the Multi-Track Operations.
You should have two tracks, one with all even numbers and one will all odd. If not, see section Saving a Track.
Select the Odd Numbers track, hold shift and select the Even numbers track (be sure to select the blue odd numbers first).
In the Graph panel, under Operations, under Multi-Graph, select the first option, and it go; select the second and hit go. Do this for each operation, and then verify the following points. The values for each operation are given for the range that is 16 in the original Even Numbers file.
For some operations, the order matters. So now select the Even Numbers track first, hold shift, and select the Odd Numbers track. Produce the tracks to verify the following:
For this test, we will use files from the quickload site.
To mimick the images exactly (optional):
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