Uploaded image for project: 'UGENE'
  1. UGENE
  2. UGENE-6238

Problems with some FASTQ files when mapping reads with BWA-MEM

    XMLWordPrintable

    Details

    • Story Points:
      2
    • Sprint:
      DEV-32-1, DEV-32-3, DEV-32-4, DEV-32-5
    • Affect Type:
      Userdefined

      Description

      Find the data for the issue on the local server.

      Scenario:

      1. Make sure "bwa" external tools is set up.
      2. Select "Tools > NGS data analysis > Map reads to reference".
      3. In the appeared dialog:
        • Set the mapping tool to "BWA-MEM".
        • Specify the reference sequence.
        • Add a FASTQ file.
        • Start the tool execution.
          Expected state: the reads are mapped to the reference.
          Current state: the result depends on the operating system, for example, there is a crash on macOS and an error message on Windows. The result also depends on on the format of the input FASTQ file, for example, it differs when the file is saved into "UTF-8, with BOM" and "UTF-8, no BOM" formats.

        Attachments

          Issue Links

            Activity

              People

              Assignee:
              dsukhomlinov Dmitrii Sukhomlinov
              Reporter:
              oigl Olga Golosova
              Assigned Tester:
              Svetlana Samoilenko
              Watchers:
              2 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: