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  1. UGENE
  2. UGENE-7105

Show symbol of the second strongest chromatogram trace

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 40
    • Component/s: None
    • Labels:
    • Sprint:
      DEV-39-1, DEV-39-2, DEV-39-3, DEV-39-4, DEV-39-5, DEV-39-RELEASE, DEV-40-1
    • Affect Type:
      Userdefined

      Description

      Synopsis: Symbols corresponds to the chromatogram with the strongest signal (with the highest peak, if we talk about visualization). If this symbol is different from the corresponding one in the reference, then it's highlighted and "mutation" is visible. But, sometimes a chromatogram besides the highest peak has one more strictly visible, second highest peak (example - the attached image, read 2, symbol 176 - the blue chromatogram (C) is the highest one, but the red (T) is strongly visible too).

      Visualization: add a new tab on the right named "Reads". On this tab create the "Mutations" section. Add a checkbox called "Show mutations with lower signal" and a slider with a combobox (see the "Consensus" tab -> "Consensus mode" ->"Threshold" - you should do something which looks the same) called "Threshold" valued from 20% to 100%. The slider should be enabled only if the checkbox is checked. 

      Functionality: when the checkbox is unchecked the behavior should be like now. When it's checked, the mutations, described in the Synopsis section should be visible. The "Threshold" value shows what percentage of the "first" signal should the "second" value signal have (if the first signal has value 100, the threshold is set to 60%, than the second one should have at least 60). The "first" signal character should be replaced with the "second" one if the second one fits to the requirement.

        Attachments

        1. 20210309_DNMT3_R882.rar
          289 kB
          Dmitrii Sukhomlinov
        2. image.png
          178 kB
          Dmitrii Sukhomlinov

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              Assignee:
              dsukhomlinov Dmitrii Sukhomlinov
              Reporter:
              dsukhomlinov Dmitrii Sukhomlinov
              Assigned Tester:
              Svetlana Samoilenko
              Watchers:
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                Dates

                Created:
                Updated:
                Resolved: