Editing BioMicroCenter:Sequencing Quality Control (section)

== Why is QC Important? ==

It is very important to have a reliable measurement of the amount of starting material so that the sample can be prepared for hybridization and amplification on the flow cell. The ideal sample is a library with 10nM of successfully ligated DNA. A 1.3ng/ul, 200bp sample is approximately 10nM. 

As of July 2012 the optimum cluster range is from about 250,000 to 350,000 per tile on the GAIIx and 700,000-900,000 on the HiSeq. It is crucial that we have accurate concentrations on hand to prevent under- and over-clustering. If a sample is loaded at too high of a concentration or the fragment size is highly variable the sequencers will not be able to distinguish between clusters properly, resulting in the loss of reads. If the sample is too dilute the optimum number of reads per lane will not be achieved. Having reliable concentration measurements allows us to optimize the number of reads per lane and maximize the quality of data produced.

[[Image:HiSeqStats.png|thumb|right|HiSeq QC]]

For sample results generated with BioMicro Center's QC methods, please view our[[Media:ABRF2011_poster_final.pdf| QC POSTER]] 

Much effort and time has been spent on optimizing loading concentrations and accounting for variations in various library prep techniques to generate optimal cluster densities on the HiSeq. The following plot shows the optimal cluster range we aim for in each experiment to efficiently generate reads with a high pass filter percentage: