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?
Thanks!
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?
Thanks!
Comment