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General Function Checklist
Annotation Track Operators
Note: Be sure to look at the user guide pages linked here. Skim them to make sure that the topics they cover are represented here (if not add points here as needed). Read enough to ensure that the instructions and explanations are clear, and the page has accurate information and generally appears up-to-date.
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See Users Guide pages:
single track - output an annotation track
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- Open the
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- A_thaliana_Jun_2009 genome.
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- Go to this region:
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- Chr1:2,992,975-3,012,448
- Load the TAIR10 mRNA
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- track via the Available Data section (IGB Quickload > TAIR10 other annotations
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- ).
- Select the
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- Annotation tab at the bottom of IGB, and look for the Operations box.
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single track
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- copy
- Select the ( - ) track and select
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- Copy, hit
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- Go.
- Select the ( + ) track, select
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- Copy, hit
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- Go.
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- Combine the ( - ) and ( + ) tracks into one using the
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- +/-
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- checkbox.
- Select the
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- +/-
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- track, select
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- Copy, hit
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- Go.
- In the
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- Annotation tab, use Select All, and under Strand, check the Arrow option (to make visual verification easier)
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- The tracks produced match this the image : above (color matching the colors is optional)the .
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- The track names for the new tracks indicate which track they were made from AND which strand ( -, + or +/- )
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- The tracks made from only one strand have only have the annotations from that strand.
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- The track made from both strands has annotations from both strands.
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single track - not, summary
- Delete the tracks you just created.
- Split the TAIR10 mRNA track back into separate - and + tracks.
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- Select the ( - ) track, select Not, hit Go.
- Select the ( + ) track, select Not, hit Go.
- Recombine the - and + tracks.
- Select the ( +/- ) track, select Not, hit Go.
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- Repeat all of the above for the
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- Summary operation.
- Color the tracks that were made from the ( - ) strand pink and the ( + ) blue
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- for visual verification
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- .
- Your IGB looks like the image above.
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multi track
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- output an annotation track
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- Using the combined (+/-) TAIR10 mRNA track, run the Summary operation and the Not operation.
- Hide the original track and highlight the two newly created tracks (hold shift and click each one) --Select the
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- Not
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- track first.
- Perform each of the multi-track operations:
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xor
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- A not B
- B not A
- Intersection
- Union
Xor
- Your IGB looks like the image above.
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- Track labels include the name names of the operation and the input tracks.
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- Visually inspect the Each track is identical to the "Not" track, or identical to the "Summary" track, or completely solid, as appropriate.
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- Delete the tracks you just created.
- Using the
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- split ( - ) and ( + ) TAIR10 mRNA track, perform each of the multi-track operations:
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xor
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- A not B
- B not A
- Intersection
- Union
- Xor
- Your IGB looks like the image above (Particularly notice the area around the zoom stripe, it highlights the difference between Union and Xor.)
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single track - output a graph track from a bed file
Keep using the Arabidopsis thaliana June 2009 genome annotations file, keep using this region: Chr1:2,992,975-3,012,448
- Use the + and - tracks separately to run each of these operations (this produces 4 graph tracks).
- depth (all) (single track)
- depth (start)
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- (single track)
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- Repeat this by selecting both the - and the + track at the same time (hold shift) and
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- selecting the above single track operations.
- The results should be identicalof step 1 and 2 above are identical.
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- Select one of the depth (all) graphs.
- In the
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- Graph panel,
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- choose Thresholding...
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- Set
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- Visibility to On.
- Slide the By Value slider
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- back and forth.
- The little blocks appear and disappear as the line touches the graph.
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- verify that the The values in the graph track correspond to counts of annotations that cover each location.
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Click Make Track
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- The new track looks correct based on the By Value threshold that you set.
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- Verify that the The new track has an appropriate label ( that indicates what threshold was used to create it).
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- See image
- Your IGB looks similar to the image above (notice that the depth (start) graphs have data in a 1-base-wide area at the start of the annotations, and where there is only 1 annotation, the graph has a height of of 1).
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single track - output a graph track from a bam file (part 1)
Keep using the Arabidopsis thaliana June 2009 genome annotations file. Go to this region: Chr1 Chr1:2,998,442-3,001,453
From the RNA-Seq quickloadQuickload in the Available Data section, add the RNA-Seq / Pollen SRP022162 / Reads / Pollen alignments file.
Click Load DataClick , then Load Sequence.
Select the Pollen alignments track and run the following single track operations:
- Select Find Junctions, enter 5, hit go.
- Select Find Junctions, enter 10, hit go.
- Select Find Junctions (tophat), enter 5, hit go.
- Select Find Junctions (tophat), enter 10, hit go.
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- Your IGB looks like the image above (*Read the junctions user guide page
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- for more details).Check the
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Right click blank space in any of the tracks, then click Optimize Track Height.
- The sizes of the blocks for the Find Junctions tracks (it should match the value you entered); the find junctions Find Junctions (tophat) results will not all have the same block size.(Right click track > optimize track height. This will show all of the reads.)
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- Verify that the The count above each junction is equal to the number of reads that matched that gap.
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- Find someplace where the matching Find Junctions operation using value 5 and value 10 have different scores. Identify the read(s) that matches that junction, and where where one side of the read is between 5 and 10 bases.
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single track - output a graph track from a bam file (part 2)
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- Open the H_Sapiens_Dec_2013 genome.
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- Add the smoke testing
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- Quickload using the Available Data section: http://igbquickload.org/smokeTestingQuickload/
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- Add the
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- Bam (binary alignment with index) track to IGB.
- Go to this region:
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- chr1:2,180,492-2,180,751
- Click Load
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- Data, then click Load Sequence.
- Select the Bam
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- (binary alignment with index) track and do the following single track operations:
- depth (all) (single track)
- depth (start) (single track)
Mismatch Graph
Mismatch Pileup Graph
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- Your IGB looks like the image above.
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- Zoom out
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- to the following coordinates: chr1:2,180,361-2,180,883
- Click Load Data (do not load sequence). Load data a second time if needed, but not a third.
- verify that the The sequence is loaded as needed after a max of two time clicking Load Data.
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Go to this region: chr1 chr1:3,785,135-3,785,276, it should look like this:
- Your IGB looks like the image above.
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Users Guide
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Review the users guide pages.
Each page has accurate information and generally appears up-to-date.
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