Update--
Quality on first read was low and got an "N" in up to half the reads at positions 12, 20, 21, and 24. Indexing read was fine. The instrument completely lost focus on 2nd read (100 nt read) so I got nothing. That read started reading into the specific amplicon reverse primer which I thought would be okay because clusters had been found on the first read. Apparently not true. Doesn't matter for this library but eventually want to join longer reads. Am trying again next run with 20% spike in of high complexity library and 50% lower cluster density.
We've had the solenoid change-out and the s/w upgrades (just before this run) and bubble-related loss of focus should not be entire lane starting with cycle 1 (or so Illumina claims). This was 100% loss, not a few percent.
Quality on first read was low and got an "N" in up to half the reads at positions 12, 20, 21, and 24. Indexing read was fine. The instrument completely lost focus on 2nd read (100 nt read) so I got nothing. That read started reading into the specific amplicon reverse primer which I thought would be okay because clusters had been found on the first read. Apparently not true. Doesn't matter for this library but eventually want to join longer reads. Am trying again next run with 20% spike in of high complexity library and 50% lower cluster density.
We've had the solenoid change-out and the s/w upgrades (just before this run) and bubble-related loss of focus should not be entire lane starting with cycle 1 (or so Illumina claims). This was 100% loss, not a few percent.
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