Those of you have just gotten MiSeq and intending to use them to help dial in cluster densities for their HiSeqs, check your MyIllumina: Bulletin. Especially
Can anyone support or contradict this? We just got the MiSeqs, so this would be mission critical for us. I guess we tend to load our HiSeq (or, previously, HiScanSQ) at 12 pM [wrong, it was loaded at 10 pM] (assay by SYBR-green KAPA qPCR with Illumina phiX as our concentration standard.) That tended to land us in the 600-800 Kclusters/mm^2 on the HiScanSQ. On the HiSeq, the phiX control lanes at 12 pM came in way low (450 K clusters/mm^2) whereas the libraries we titrated with them came in higher than expected: 700-1100K clusters/mm^2. But that could just be normal variation.
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Phillip
Cluster efficiency – Due to differences in the cluster generation chemistry, the MiSeq flowcells typically cluster at approximately 50% higher cluster density than the same library concentration loaded on a HiSeq flow cell (i.e. a library concentration that yields 750/mm2 clusters on a MiSeq will result in approximately 500/mm2 on a HiSeq).
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Phillip
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