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Old 12-12-2018, 02:16 AM   #1
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Location: South Africa

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

Good day,

Can anyone advise me on the following regarding a recent amplicon sequencing run on the Illumina MiSeq:

What would be the cause for a relatively low intensity and low quality Index 1 read (i7) compared to Read 1, Index 2 (i5) and Read 2?

The nucleotides at each position within the indices used were balanced.

The run was quite under-clustered.

Also, other than potential dilution problem, what are other reasons for obtaining a significantly higher alignment of Phix compared to what was originally spiked?

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Old 12-12-2018, 06:11 PM   #2
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Did you use custom sequencing primers for any of the reads?
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