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!
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!