Athurva Gore/LabNotes/2009-8-26
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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 --> (RUNNING)
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