Hi All,
I have a question related to cluster density as it relates to getting consistent results between different runs. I am doing RNA-seq using Miseq v3 and when I first started, I got cluster densities around 700K and 950K from loading my DNA samples at 13.5pm for my first two runs. I tried bumping up to 15pm loading concentration to increase cluster density and my cluster density dropped (450K). This is confusing since loading more DNA have should lead to higher cluster density.
From that, I can reasonably infer that loading my pool at 13.5pM for my last run would have given me significantly lower cluster density than what I got from the first two runs. I ran a different set of libraries for each run but the prep kit, quantification and pooling strategy were the same. Does anyone have experience with different libraries/pools generated and quantified using the same exact protocol clustering at different densities even when loaded at the same concentration?
I have a question related to cluster density as it relates to getting consistent results between different runs. I am doing RNA-seq using Miseq v3 and when I first started, I got cluster densities around 700K and 950K from loading my DNA samples at 13.5pm for my first two runs. I tried bumping up to 15pm loading concentration to increase cluster density and my cluster density dropped (450K). This is confusing since loading more DNA have should lead to higher cluster density.
From that, I can reasonably infer that loading my pool at 13.5pM for my last run would have given me significantly lower cluster density than what I got from the first two runs. I ran a different set of libraries for each run but the prep kit, quantification and pooling strategy were the same. Does anyone have experience with different libraries/pools generated and quantified using the same exact protocol clustering at different densities even when loaded at the same concentration?
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