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  1. IGB
  2. IGBF-4013

Investigate: Exporting mismatch graph tracks

        Details

        • Type: Task
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
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          Description

          Situation: IGB has the ability to export tracks to a file on the user's computer. To do this, a user would right-click on the track label of the track they'd like to save and click Save Track As.... We've discovered a case where this option isn't available yet it should be, and that is in the case of exporting mismatch graphs.

          Below is a step-by-step guide for creating a mismatch graph and attempting to export it:

          • Start IGB
          • Open the A_thaliana_Jun_2009 genome
          • In the Available Data section, open the following file: RNA-Seq > Auxin arf19 > Reads > arf19-4 IAA alignments
          • Navigate to Chr5:7,866,559-7,870,566
          • Click Load Data
          • Right-click on the "arf19-4 IAA alignments" track label
          • Click Track Operations > Mismatch Graph
          • Right-click on the "Mismatch Graph: arf19-4 IAA alignments (+|-)" track label
          • See that the option to Save Track As... is grayed out.

          Task: Investigate exporting mismatch graph tracks.

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              nfreese Nowlan Freese added a comment - - edited

              Reviewing Deepthi's branch on Mac.

              Able to save a mismatch graph as a bedgraph.

              Some changes I would like:

              • The mismatch graph coordinates in the mismatch bedgraph (2nd and 3rd columns) are the same. I think they need to be off by one to display correctly in IGB. For example: 7870605 7870605 should be 7870605 7870606
                • Also similar to depthgraph, the coordinates for the mismatch can be larger than 1. For example, if from position 1-10 there was a value of 5, then we would need a single line with coordinates 1 10 and a value of 5.
              • There are a lot of values with 0 in the fourth column of the mismatch bedgraph. I think we can omit these from the bedgraph file similar to when we export a depthgraph.
              • The mismatch pileup graph save track option should remain grayed out if possible. If I do save a track from the mismatch pileup it is creating what looks like a depth graph, which may be confusing to the user.

              I would be curious to see/understand the logic for how the depthGraph files are being exported by IGB.

              Show
              nfreese Nowlan Freese added a comment - - edited Reviewing Deepthi's branch on Mac. Able to save a mismatch graph as a bedgraph. Some changes I would like: The mismatch graph coordinates in the mismatch bedgraph (2nd and 3rd columns) are the same. I think they need to be off by one to display correctly in IGB. For example: 7870605 7870605 should be 7870605 7870606 Also similar to depthgraph, the coordinates for the mismatch can be larger than 1. For example, if from position 1-10 there was a value of 5, then we would need a single line with coordinates 1 10 and a value of 5. There are a lot of values with 0 in the fourth column of the mismatch bedgraph. I think we can omit these from the bedgraph file similar to when we export a depthgraph. The mismatch pileup graph save track option should remain grayed out if possible. If I do save a track from the mismatch pileup it is creating what looks like a depth graph, which may be confusing to the user. I would be curious to see/understand the logic for how the depthGraph files are being exported by IGB.
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              sjagarap saideepthi jagarapu (Inactive) added a comment - - edited
              • Data file formats can be found in - https://genome.ucsc.edu/FAQ/FAQformat.html
              • Enabled save track as option, which on click exports mismatched graph in bedgraph format.
              • Loaded exported local file by opening it in track and compared it with mismatched graph in track, verified that it exactly matches as shown in attached screenshot.

              Worked Branch - https://bitbucket.org/lorainelab-deepthi/integrated-genome-browser/branch/IGBF-4013

              Show
              sjagarap saideepthi jagarapu (Inactive) added a comment - - edited Data file formats can be found in - https://genome.ucsc.edu/FAQ/FAQformat.html Enabled save track as option, which on click exports mismatched graph in bedgraph format. Loaded exported local file by opening it in track and compared it with mismatched graph in track, verified that it exactly matches as shown in attached screenshot. Worked Branch - https://bitbucket.org/lorainelab-deepthi/integrated-genome-browser/branch/IGBF-4013

                People

                • Assignee:
                  sjagarap saideepthi jagarapu (Inactive)
                  Reporter:
                  pkulzer Paige Kulzer
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                  • Created:
                    Updated: