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=Analysis of 9 technical replicates from HL111 (NA12156)= * Noi performed 9 capture reactions from the same bisulfite converted gDNA, and this library was captured and sequenced in HL111. * Noi mapped all the data and created the methylation matrix file from the 9 BED files requiring data from at least 7 of the 9 replicates. ** 7 data points is good enough to determine the methylation distribution and variance of a captured site. ** In total, there were : 412,476 sites captured by at least 7 samples. ** However the standard deviation for ~25% of the sites were > 0.1. * Checking the QC values for this dataset: rep1 N=9175 r=0.9111 rep2 N=13414 r=0.9292 rep3 N=8385 r=0.9157 rep4 N=16172 r=0.9754 rep5 N=17041 r=0.9738 rep6 N=9770 r=0.9273 rep7 N=15372 r=0.9312 rep8 N=12460 r=0.8802 rep9 N=12389 r=0.8949 * Why does both N and r values vary so much? * As the average QC drop, which sites become more variable? * Where these sites variable sites localized? * We can go back to low quality dataset and mask these variable sites.
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