Athurva Gore/LabNotes/2009-8-26: Difference between revisions

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* Upon looking at SNP distribution, found that bases after #25 had very high false positive rate
* 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
* 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=
=PGP High False Positive Data=
* Plotted SNP distributions for PGP1 and PGP2 data (06022009, Lanes 1 and 2)
* Plotted SNP distributions for PGP1 and PGP2 data (06022009, Lanes 1 and 2)

Revision as of 23:18, 26 August 2009

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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