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  • Index 1 read (i7) - Low Intensity & Low Quality??

    Good day,

    The following question concerns an amplicon sequencing run on the Illumina MiSeq instrument.

    What would be the reason for a much lower intensity & lower quality specifically for Index 1 read (i7) compared to Read 1, Index read 2 (i5) and Read 2?

    It was ensured that nucleotide at each position in the index reads used were balanced.

    Also, other than a possible dilution error, what other reason would be the cause of obtaining a much higher alignment of Phix than originally spiked?

    The run was quite under-clustered.

    Thanks!

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