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  • Protaeus
    Member
    • Aug 2010
    • 21

    #1

    PicardTools IlluminaBaseCallsToSam

    I was going to run the subject mentioned (and probably not-oft used) tool in Picard that can demultiplex basecalls (i.e. barcodes run) into sam's or bam's. I was wondering how it deals with bcl files, if at all. And, if not, is there a suggested work-around? I generally convert the bcl's into qseq's into a separate folder, which means that it is not in the original run folder...which I'd imagine could pose a problem?

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