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  1. IGB
  2. IGBF-3517

Investigate: User-reported problem with reads visualization

        Details

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

          Description

          User (email address Reinhold_C1@ukw.de) contacted us with this problem:

          Dear Ms. Loraine,

          I am currently facing an issue while attempting to plot reads for a specific gene in IGB. Despite ensuring that both the BAM and the BAI files are in the same folder, searching for the specific gene before loading my bam file and clicking on the “load data” button, I find myself unable to visualize the reads. I’ve also tried resetting the preferences as recommended in the troubleshooting section of the user´s guide, without success. Do you have any other suggestions as to why I may be unable to see my reads when loading my bam files ?

          Thank you for your help.

          Best,

          Colette Reinhold, M.Sc
          Universitätsklinikum Würzburg
          Neurologische Klinik und Poliklinik
          AG Prof. Dr. Ip
          Josef-Schneider-Str.11
          97080 Würzburg

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              ann.loraine Ann Loraine added a comment -

              Sent this reply:

              I'm sorry you are having trouble with IGB and visualizing the BAM file reads.

              I will try to help.

              For the next steps please do this:
              Start IGB
              Go the gene you were looking at before and again try to load the reads
              After doing this, select the "Log" tab (lower part of IGB)
              Click "Copy All to Clipboard"
              Paste the contents into a file or an email, and it send it to me
              Regards,

              Ann Loraine

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              ann.loraine Ann Loraine added a comment - Sent this reply: I'm sorry you are having trouble with IGB and visualizing the BAM file reads. I will try to help. For the next steps please do this: Start IGB Go the gene you were looking at before and again try to load the reads After doing this, select the "Log" tab (lower part of IGB) Click "Copy All to Clipboard" Paste the contents into a file or an email, and it send it to me Regards, Ann Loraine
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              ann.loraine Ann Loraine added a comment -

              The user sent a Word document with log messages. No error messages were printed. I asked for them to send me the file somehow.

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              ann.loraine Ann Loraine added a comment - The user sent a Word document with log messages. No error messages were printed. I asked for them to send me the file somehow.
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              ann.loraine Ann Loraine added a comment -

              Waiting on user to share the file with us.

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              ann.loraine Ann Loraine added a comment - Waiting on user to share the file with us.
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              ann.loraine Ann Loraine added a comment -

              User replied that they will ask their boss about sharing the file and get back to us.
              Moving to Backlog.

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              ann.loraine Ann Loraine added a comment - User replied that they will ask their boss about sharing the file and get back to us. Moving to Backlog.

                People

                • Assignee:
                  Unassigned
                  Reporter:
                  ann.loraine Ann Loraine
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                  Dates

                  • Created:
                    Updated: