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Old 12-11-2018, 11:41 PM   #1
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Location: South Africa

Join Date: Jul 2018
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Default 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.

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