Pmiguel,
two reasons i can think of lower than expected cluster density for unamplified high GC bacteria:
1. missing adaptor on the fragment. amplified library has already filtered out those fragments without adp on both ends.
2. High GC fragment doesn't amplify effectively during cluster generation even if it has perfect adp on both ends. the very high GC fragment probably has dropped out in the amplified library already.
ECO,
Do you see discrepancy between the qPCR quantitation and bioanalyzer for amplified and unamplified libraries?
two reasons i can think of lower than expected cluster density for unamplified high GC bacteria:
1. missing adaptor on the fragment. amplified library has already filtered out those fragments without adp on both ends.
2. High GC fragment doesn't amplify effectively during cluster generation even if it has perfect adp on both ends. the very high GC fragment probably has dropped out in the amplified library already.
ECO,
Do you see discrepancy between the qPCR quantitation and bioanalyzer for amplified and unamplified libraries?
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