Hi,
I thought I gotten a feeling from looking at live thumbnails during scan as to the average cluster density we would obtain, but our latest run has thrown me - density looked similar at cycle 1 to successful runs previous (HiScanSQ) but at cycle 2 the thumbnails show FAR fewer clusters than cycle 1 - if I were judging on C1 I would expect ~900k/mm2, on C2 I'd say less than 300k/mm2!!.
The clusters are nowhere near as bright as they were at C1 either. Anyone seen such a dramatic dropoff in density across cycles before? These are low diversity libraries (with 5% PhiX spike) but that shouldn't affect the live thumbnail, should it? It looks green no matter which base is added...
Matt
I thought I gotten a feeling from looking at live thumbnails during scan as to the average cluster density we would obtain, but our latest run has thrown me - density looked similar at cycle 1 to successful runs previous (HiScanSQ) but at cycle 2 the thumbnails show FAR fewer clusters than cycle 1 - if I were judging on C1 I would expect ~900k/mm2, on C2 I'd say less than 300k/mm2!!.
The clusters are nowhere near as bright as they were at C1 either. Anyone seen such a dramatic dropoff in density across cycles before? These are low diversity libraries (with 5% PhiX spike) but that shouldn't affect the live thumbnail, should it? It looks green no matter which base is added...
Matt
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