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Old 11-18-2010, 02:20 PM   #1
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Default fastq files generated by Casava-Eland

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?
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Old 11-19-2010, 04:56 AM   #2
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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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