Athurva Gore/LabNotes/2009-8-18: Difference between revisions

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>Ajgore
(New page: {{ AGLabEntry|2009-8-17|2009-8-19 }} =Probe Generation= * '''DONE''' ** KKESH72 ** RPLCACRD ** CpG-SNP set (with 80 bp gap) ** FlyDup936 ** A-to-I Probes for Erez and Billy ** LeeCancer (...)
 
>Ajgore
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* Currently:
* Currently:
** Running script to separate our SNP calls and 1KG SNP calls by in-range and out-of-range
** Running script to separate our SNP calls and 1KG SNP calls by in-range and out-of-range
* For our SNP calls:
** FOUND THAT 3190/20762 were NONSPECIFIC
** ~85% specific capture
* Want to separate false positives from true positives in our SNPs.
* Want to separate false positives from true positives in our SNPs.
* NEXT STEP:
* NEXT STEP:

Revision as of 16:59, 18 August 2009

Navigation

Probe Generation

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

Exome SNPs - NA12878

  • Currently:
    • Running script to separate our SNP calls and 1KG SNP calls by in-range and out-of-range
  • For our SNP calls:
    • FOUND THAT 3190/20762 were NONSPECIFIC
    • ~85% specific capture
  • Want to separate false positives from true positives in our SNPs.
  • NEXT STEP:
    • Look at IPS data; plot quality and coverage of SNPs.
    • Run bowtie on runs from NA12878 that have high false positives
    • See if there is a pattern; can we separate these false positives out somehow?