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

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>Ajgore
(New page: {{ 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 ...)
 
>Ajgore
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=PGP High False Positive Data=
=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'''

Revision as of 22:35, 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

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