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  • casava
    Junior Member
    • Nov 2010
    • 1
    #1

    fastq files generated by Casava-Eland

    Hi,
    I know the eland export files generated from Eland in the Casava software contain recalibrated quality scores. Does anyone know if the fastq files generated by Casava also contain the recalibrated quality score or the original quality scores?
    Thanks,
    Casava
    Tags: None
    • kmcarr
      Senior Member
      • May 2008
      • 1181
      #2
      It is my understanding that the Illumina pipeline no longer performs quality score re-calibration, and Illumina generally recommends against it.

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