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{{ AGLabEntry|2009-8-25|2009-8-27 }} =IPS and Cancer= * IPS data still had a large number of false positives, despite filtering * Upon looking at SNP distribution, found that bases after #25 had very high false positive rate * Reran filter, discarded reads with SNPs after base 25 ** IPS Set: 11314 in dbSNP, 2144 non-dbSNP --> 9370 in dbSNP, 1099 non-dbSNP ** Fibroblast Set: 9254 in dbSNP, 2504 non-dbSNP --> 7355 in dbSNP, 1187 non-dbSNP * The number of non-dbSNP misses needs to be reduced further without removing more hits ** How to accomplish this? *** Reduce quality of SNPs found towards the end of reads by a certain factor *** Trim reads when a SNP is found? *** Trim all reads and check data? *** Be skeptical of a train of SNPs? Perhaps throw out reads with more than two SNPs? =PGP High False Positive Data= * Plotted SNP distributions for PGP1 and PGP2 data (06022009, Lanes 1 and 2) * Found a similar issue with SNP distributions as in the IPS sets * However, these used longer reads; errors seem to start around read 50 ** '''INCLUDE GRAPHS OF SNPDIST HERE'''
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