Athurva Gore/LabNotes/2009-8-12: Difference between revisions

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=IPS and Cancer=
=IPS and Cancer=
* DF6-9-9 IPS line has preliminary data available.
* Lane 1 is IPS, Lanes 2 and 3 are the corresponding fibroblast (Lane 3 has no size-selection)
* Located on genome-miner in:
** /home/kunzhang/Exome/Solexa/090805_HL003
* Dr. Zhang wrote two scripts for preliminary processing
** /home/kunzhang/Exome/scripts/variantCallerSoapSam.pl - calls consensus sequence using SOAP and SAM
** /home/kunzhang/Exome/scripts/pileup2variantsPair.pl - identifies variations present given two consensus sequences
* http://docs.google.com/present/edit?id=0AZnKSQ9Jqu6_ZDVqcWd6cF80NGRiOGZrNWNn&hl=en
** Lane 2 has many more homozygous calls than Lane 3
** EITHER:
*** (A) Lane 3 has many more sequencing errors
** OR:
*** (B) Lane 2 is only amplifying one allele.
* Dr. Zhang thinks it is option (A).  I am not sure how size selection could do this; investigate.

Latest revision as of 21:24, 12 August 2009

Probe Generation[edit]

  • DONE
    • KKESH72
  • CURRENTLY RUNNING:
    • FlyDup901
    • FlyDup936
    • RPLCACRD
    • CpG-SNP set (with 80 bp gap)
  • TO RERUN:
    • FlyDup5279
    • LeeCancer (on opposite strand to target cDNA)
    • LeeXGenes (on opposite strand to target cDNA)
    • ZhangSNP (on opposite strand to target cDNA)
    • TDMR Set (Also check if out-of-memory happens again...maybe run on Miner?)

IPS and Cancer[edit]

  • DF6-9-9 IPS line has preliminary data available.
  • Lane 1 is IPS, Lanes 2 and 3 are the corresponding fibroblast (Lane 3 has no size-selection)
  • Located on genome-miner in:
    • /home/kunzhang/Exome/Solexa/090805_HL003
  • Dr. Zhang wrote two scripts for preliminary processing
    • /home/kunzhang/Exome/scripts/variantCallerSoapSam.pl - calls consensus sequence using SOAP and SAM
    • /home/kunzhang/Exome/scripts/pileup2variantsPair.pl - identifies variations present given two consensus sequences
  • http://docs.google.com/present/edit?id=0AZnKSQ9Jqu6_ZDVqcWd6cF80NGRiOGZrNWNn&hl=en
    • Lane 2 has many more homozygous calls than Lane 3
    • EITHER:
      • (A) Lane 3 has many more sequencing errors
    • OR:
      • (B) Lane 2 is only amplifying one allele.
  • Dr. Zhang thinks it is option (A). I am not sure how size selection could do this; investigate.