Very specific question but has anyone encountered low read quality in only read 2 on the MiSeq using a 500 cycle v2 kit with run configuration of 2x250?
I have does 3 consecutive runs now with two different labs and all 3 are giving me the same phenotype with drastic read 2 quality drop off. The runs do use custom primers but all have been used by collaborators with success and Tm's have been checked. I have done similar runs with the 300 cycle kit with no issue.
I have does 3 consecutive runs now with two different labs and all 3 are giving me the same phenotype with drastic read 2 quality drop off. The runs do use custom primers but all have been used by collaborators with success and Tm's have been checked. I have done similar runs with the 300 cycle kit with no issue.
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