Compare Pipeline 1.4vs1.3

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Comparing Solexa Pipeline Version 1.4 vs 1.3

Conclusion: 1.4 seems to sometimes do a better job detecting raw clusters at lower densities.
Raw reads.JPG
Conclusion: As expected, 1.4 is able distinguish close clusters better than 1.3, hence intensities/clusters are more "pure".
Fitered reads.JPG
Conclusion: Number of filtered reads for 1.3 at a cluster density of around 100k (10 million reads) and drops somewhere between 160 - 170k. 1.4 seems to start dropping around 180k but in general it gives more reads as well as better quality reads.
Density vs fitered reads.JPG
Conclusion: Base quality starts to decrease drastically around 190k for 1.4. The optimal cluster density potentially is between 180 - 190k.
Conclusion: Error Rates (to be added).
Conclusion: Alignment Rate (to be added).