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  1. IGB
  2. IGBF-1427

Fix paired end overlap

        Details

        • Type: Bug
        • Status: To-Do (View Workflow)
        • Priority: Critical
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Looking at the 1/14436308-14438564.bam file from IGBF-1291, there are occurrences of paired reads overlapping each other inappropriately. After extracting reads, issue seems to be with reads occurring multiple times in file or with the bitwise flag where reads have unmapped mates.

          For example look at the following read in the file problemReads.sam
          HK2WYCCXX160124:2:1205:27417:57846

          This read appears three times. Two of the reads are mates to each other (look at column 8) but are not mapped in a proper pair, while the other does not have a mate. When viewed in IGB with show as paired, the pair overlaps other reads.

          Might have to do with how IGB renders pairs that are not mapped in proper pair.

            Attachments

            1. notShowAsPaired.png
              notShowAsPaired.png
              102 kB
            2. problemReads.bam
              10 kB
            3. problemReads.bam.bai
              8 kB
            4. problemReads.sam
              139 kB
            5. showAsPaired.png
              showAsPaired.png
              101 kB

              Activity

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              nfreese Nowlan Freese created issue -
              aloraine Ann Loraine made changes -
              Field Original Value New Value
              Workflow Loraine Lab Workflow [ 18133 ] Fall 2019 Workflow Update [ 18912 ]
              aloraine Ann Loraine made changes -
              Workflow Fall 2019 Workflow Update [ 18912 ] Revised Fall 2019 Workflow Update [ 21039 ]
              Status Open [ 1 ] To-Do [ 10305 ]
              aloraine Ann Loraine made changes -
              Assignee Ann Loraine [ aloraine ]
              aloraine Ann Loraine made changes -
              Rank Ranked higher
              aloraine Ann Loraine made changes -
              Epic Link IGBF-1765 [ 17855 ]
              aloraine Ann Loraine made changes -
              Story Points 2
              aloraine Ann Loraine made changes -
              Priority Minor [ 4 ] Critical [ 2 ]
              aloraine Ann Loraine made changes -
              Rank Ranked higher

                People

                • Assignee:
                  Unassigned
                  Reporter:
                  nfreese Nowlan Freese
                • Votes:
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                  Watchers:
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                  Dates

                  • Created:
                    Updated: