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===Grouping of probes=== * Only UPENN data had capture from Sub6 and Sub7, but I have only mapped one dataset so far. I will need to go back and map additional datasets and consider Sub6 and Sub7 separately 1) Probes that never get any capture in any dataset Exp1-3 23,931 Sub1 40 Sub2 34 Sub3 246 Sub4 213 Sub5 6,137 ================ 30,601 probes out of 237,128 (12.9%) 2) Probes that are inconsistent across datasets I defined these as having 0 capture for at least 1 dataset and a normalized standard deviation of capture of 0.28 or greater To get the normalized standard deviation of capture: calculate the standard deviation of coverage across multiple captures and divide by range of capture (max capture coverage - min capture coverage). I need to normalize the capture coverage within each sample by the total reads mapped. 3) Probes that are consistent across datasets and can further be subset by level of efficiency
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