UGENE
  1. UGENE
  2. UGENE-5863

Wrong identity filtering in Sanger

    Details

    • Story Points:
      1
    • Tests Type:
      GUI automatic
    • Epic Link:
    • Sprint:
      DEV-29-1, DEV-29-2
    • Affect Type:
      Userdefined

      Description

      The Sanger reads mapping algorithm in UGENE has two steps:

      1. Finding of results with BLAST.
      2. Adjustment of the result with the Smith-Waterman algorithm.

      In version 1.28 the value of the "Mapping min identity" parameter in the "Map Sanger Reads to Reference" dialog applies to the first step of the algorithm only. The identity should be checked after the two steps instead.

      Note also, that the parameter shouldn't be misinterpreted with the "Identity" value of a BLAST result. The latter one is the identity between the found part of a read with the reference. The "Mapping min identity" parameter specifies required identity between the whole read and the reference.

        Issue Links

          Activity

          Hide
          Olga Golosova
          added a comment -

          Note that the "Mapping min identity" will be renamed to "Mapping min similarity" in UGENE-5868, as besides substitutions the Sanger reads mapping algorithm also takes into account insertions and deletions.

          See also this description of the identity and similarity terms.

          Show
          Olga Golosova
          added a comment - Note that the "Mapping min identity" will be renamed to "Mapping min similarity" in UGENE-5868 , as besides substitutions the Sanger reads mapping algorithm also takes into account insertions and deletions. See also this description of the identity and similarity terms .
          Hide
          Olga Golosova
          added a comment - - edited

          I've updated the description of the mapping task and the dialog in on the "Mapping Reads to Reference" documentation page. During the review please update the dialog screenshot and add a screenshot of the report.

          Show
          Olga Golosova
          added a comment - - edited I've updated the description of the mapping task and the dialog in on the "Mapping Reads to Reference" documentation page . During the review please update the dialog screenshot and add a screenshot of the report .
          Hide
          Eugenia Pushkova
          added a comment -

          GUI test is GUITest_common_scenarios_sanger::test_0007

          Show
          Eugenia Pushkova
          added a comment - GUI test is GUITest_common_scenarios_sanger::test_0007
          Hide
          Yuliya Algaer
          added a comment -

          Reviewed.

          Show
          Yuliya Algaer
          added a comment - Reviewed.

            People

            • Assignee:
              Eugenia Pushkova
              Reporter:
              Eugenia Pushkova
              Assigned Tester:
              Aleksey Tiunov
            • Votes:
              0 Vote for this issue
              Watchers:
              3 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved:

                Agile