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  • KarinVL
    Junior Member
    • Sep 2018
    • 1
    #1

    Using Ion Reporter for data from other platforms

    I have been using Ion Reporter (together with our Ion PGM and S5) for several years now and am really happy with this software.

    Now I received data from an Illumina platform and was hoping to analyse this with the same software.

    Has anybody else tried this before? And did you succeed?

    The fastq files I got were aligned with bwa mem. The uploading of the bam files went allright, but when trying to analyse them, I get an error message about the SamReadGroupRecords List being null or empty.

    Anybody has any suggestions?
    Tags: None
  • torben
    Member
    • Oct 2012
    • 21
    #2
    You can add read group info to your bam-files using Picard's AddOrReplaceReadGroups (https://broadinstitute.github.io/pic...laceReadGroups). You can also add it during alignment with the -R option to bwa.

    More info about Read Groups here: https://software.broadinstitute.org/...le.php?id=6472

    Comment

    • prat824
      Junior Member
      • Jul 2011
      • 2
      #3
      Hi - did you find an answer? were you able to use Ion Reporter to analyze illumina data?

      Comment

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