Observe that:
- The Diff Inverse Inverse track has all 0-values. Notice that the top and bottom of the y-axis for this track in the image above are 0.
- The shapes and names of tracks corresponds to the image above.
- The Diff Inverse Inverse track has all 0-values. Notice that the top and bottom of the y-axis for this track in the image above are 0.
- The shapes and names of tracks corresponds to the image above.
- The Diff Inverse Inverse track has all 0-values. Notice that the top and bottom of the y-axis for this track in the image above are 0.
- The shapes and names of tracks corresponds to the image above.
Go to the Data Access panel and remove each of the tracks you created.
Single Track Operations - part 4 - inverse logs
Go to the Graph panel, and select the Even Numbers track.
- Select Log 2, hit Go
- Select Log 10, hit Go
- Select Log, enter 3, hit Go
- Select Natural Log, hit Go
- Select the Log 2: Even Numbers track, select the Inverse Log 2 operation, hit Go. Delete the Log2: Even Numbers track.
- Select the Log 10: Even Numbers track, select the Inverse Log 10 operation, hit Go. Delete the Log 10: Even Numbers track.
- Select the Log 3: Even Numbers track, select the Inverse Log operation, enter 3, hit Go. Delete the Log 3: Even Numbers track.
- Select the Natural Log: Even Numbers track, select the Inverse Natural Log operation, hit Go. Delete the Natural Log: Even Numbers track.
Set all created tracks to Stairstep. See image.
Verify that the created tracks look identical to the even number track (as demonstrated in the picture).
Go to the Data Access panel and remove each of the tracks you created.
Saving a 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:
- Select the Even Numbers track. In the Graph panel, under Operations, under Single-Graph, select Add, and enter 1.
- Select All graph tracks, and set them to StairStep.
- Go to the Data Access panel.
- Mac
- Change the Track Name to "Odd Numbers". Change the color (FG) to light blue.
- The new track should be called "Add 1.0: Even Numbers".
- Windows
- The new track should be called "Add 1.0: Even Numbers".
- Change the Track Name to "Odd Numbers". Change the color (FG) to light blue.
- Linux
- The new track should be called "Add 1.0: Even Numbers".
- Change the Track Name to "Odd Numbers". Change the color (FG) to light blue.
- Right click on the Odd Numbers track label area and click Save Track As... . Save the file as TrackOperationsTest2, keep the bedgraph file type.
- Add this file (the one you just created) to IGB. Click load data, and set it to StairStep.
- Mac - verify that the track read from the saved file and completely identical to the track it was made from (same color, name, values).
- Windows - verify that the track read from the saved file and completely identical to the track it was made from (same color, name, values).
- Linux - verify that the track read from the saved file and completely identical to the track it was made from (same color, name, values).
Remove the track with the yellow highlight. The two TrackOperationsTest files are what you will use to test the Multi-Track Operations.
Multi-Track Operations
You should have two tracks, one with all even numbers and one with 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 hit 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.
- Even Numbers: 16
- Odd Numbers: 17
- Sum: Odd Numbers, Even numbers: 33
- Diff: Odd Numbers, Even numbers: 1
- Product: Odd Numbers, Even numbers: 272
- Ratio: Odd Numbers, Even numbers: 1.0625
- Mean: Odd Numbers, Even numbers: 16.5
- Median: Odd Numbers, Even numbers: 16.5
- Max: Odd Numbers, Even numbers: 17
- Min: Odd Numbers, Even numbers: 16
- All track names include both input track names in the order they were select.
- Even Numbers: 16
- Odd Numbers: 17
- Sum: Odd Numbers, Even numbers: 33
- Diff: Odd Numbers, Even numbers: 1
- Product: Odd Numbers, Even numbers: 272
- Ratio: Odd Numbers, Even numbers: 1.0625
- Mean: Odd Numbers, Even numbers: 16.5
- Median: Odd Numbers, Even numbers: 16.5
- Max: Odd Numbers, Even numbers: 17
- Min: Odd Numbers, Even numbers: 16
- All track names include both input track names in the order they were select.
- Even Numbers: 16
- Odd Numbers: 17
- Sum: Odd Numbers, Even numbers: 33
- Diff: Odd Numbers, Even numbers: 1
- Product: Odd Numbers, Even numbers: 272
- Ratio: Odd Numbers, Even numbers: 1.0625
- Mean: Odd Numbers, Even numbers: 16.5
- Median: Odd Numbers, Even numbers: 16.5
- Max: Odd Numbers, Even numbers: 17
- Min: Odd Numbers, Even numbers: 16
- All track names include both input track names in the order they were select.
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:
- Even Numbers: 16
- Odd Numbers: 17
- Diff: Even Numbers, Odd Numbers: -1
- Ratio: Even Numbers, Odd Numbers: 0.94117647
- All track names include both input track names in the order they were select.
- Even Numbers: 16
- Odd Numbers: 17
- Diff: Even Numbers, Odd Numbers: -1
- Ratio: Even Numbers, Odd Numbers: 0.94117647
- All track names include both input track names in the order they were select.
- Even Numbers: 16
- Odd Numbers: 17
- Diff: Even Numbers, Odd Numbers: -1
- Ratio: Even Numbers, Odd Numbers: 0.94117647
- All track names include both input track names in the order they were select.
Joining and Splitting graphs
For this test, we will use files from the QuickLoad site.
- Select the Arabidopsis thaliana genome (June 2009)
- In the Data Access panel, find IGB Quickload / Chip-Seq / ARR10 PRJNA263839 / graphs
- Select:
- the first one (line a1 BA-treated ChIP rep1 coverage)
- the second one (line a1 BA-treated non-IP rep1 coverage)
- the seventh one (line a2 non-BA-treated ChIP coverage)
- Navigate to Chr1:8,036,457-8,056,240
- Click Load Data
- Arrange them so the green one is on top, then the pink, then the red.
- Select them in this order: pink, red, green.
- In the graph panel, select Join.
- Verify that:
- The three tracks now share a single label field called "Joined Graphs".
- The three tracks are ordered top to bottom: pink, red, green (the order of the selection)
- Windows
- The three tracks now share a single label field called "Joined Graphs".
- The three tracks are ordered top to bottom: pink, red, green (the order of the selection)
- Linux
- The three tracks now share a single label field called "Joined Graphs".
- The three tracks are ordered top to bottom: pink, red, green (the order of the selection)
- Click the little minus button [-] in the upper left corner of the joined tracks.
- Verify that:
- pink the most visible (its in front), red is the next most visible and green is in the back. (see images)
- Click the + button to expand them. The top-to-bottom order unchanged.
- pink the most visible (its in front), red is the next most visible and green is in the back. (see images)
- Click the + button to expand them. The top-to-bottom order unchanged.
- pink the most visible (its in front), red is the next most visible and green is in the back. (see images)
- Click the + button to expand them. The top-to-bottom order unchanged.
- Click the shared label area. In the graph panel, select Split.
- Mac - Verify that all tracks are separate again.
- Windows - Verify that all tracks are separate again.
- Linux - Verify that all tracks are separate again.
- Repeat the above steps using a different selection order
- Mac - verify the the order is reflected in how the tracks are stacked together.
- Windows - verify the the order is reflected in how the tracks are stacked together.
- Linux - verify the the order is reflected in how the tracks are stacked together.
To mimick the images exactly (optional):
- Go to this region: Chr1:8,036,457-8,056,240
- In the Graph panel, select all graphs, click the Height knob (no need to actually slide it).
- Select the red track and set the Max to 80.
- Select the green track only and set the Max to 30.
- Select the pink track and set the Max to 120.
Users Guide