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Old 01-25-2015, 10:05 AM   #40
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Originally Posted by andibody View Post
There should be an exact max of clusters for HiSeq 3000/4000 defined by the number of microwells (325M as stated above?).
We're getting regularly 300M reads on the upgraded 2500. If 325M is correct, the increase is not very pronounced if the shortened run durations are not countered in.
Are you sure you are comparing the same numbers (read, clusters, lanes, flow cell)? And for the HiSeq 2500 numbers are you talking about Rapid Run or V4 High Output?

The HiSeq 3000/4000 specs are 325M clusters per lane, which would be 650M reads per lane for paired end runs (using Illumina's method of counting).

The HiSeq 1500/2500 specs are 250M clusters per lane for V4 High Output (500M reads per lane). Our experience is pushing even slightly past 280M clusters per lane results in dramatic decreases in %PF and read quality.
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