Athurva Gore/LabNotes/2009-8-26

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Revision as of 00:03, 27 August 2009 by >Ajgore (→‎IPS and Cancer)
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IPS and Cancer[edit]

  • 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[edit]

  • 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