Hello Everyone,
I have done two 2*300bp runs on the Miseq with 384 multiplexed 16S libraries (derived from mice feces). For each run the quality of the reads has been really poor. I am even using 10% PhiX double what illumina recommends. For the first run I had a cluster density of 1109k/mm2 with 89% cluster passing filter and Q30 77% and this last run 1118k/mm2 passing filter of 87.7% and QC30 67%.
Have attached the results of the last run….Any idea what I can do have better runs? Or why the quality is so bad.
(I think it has to do with the mice that are producing my sample material live in a control and they should all have the same intestinal flora. )
I have done two 2*300bp runs on the Miseq with 384 multiplexed 16S libraries (derived from mice feces). For each run the quality of the reads has been really poor. I am even using 10% PhiX double what illumina recommends. For the first run I had a cluster density of 1109k/mm2 with 89% cluster passing filter and Q30 77% and this last run 1118k/mm2 passing filter of 87.7% and QC30 67%.
Have attached the results of the last run….Any idea what I can do have better runs? Or why the quality is so bad.
(I think it has to do with the mice that are producing my sample material live in a control and they should all have the same intestinal flora. )
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