Athurva Gore/LabNotes/2009-8-18

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Revision as of 23:17, 18 August 2009 by >Ajgore (→‎NEXT STEPS:)
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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
  • Check numbering of new probes
    • Appears to be slightly inaccurate as well.
    • For residue coordinate system:
      • End position should be increased by 1
      • Start position should be increased by 2
    • For space coordinate system:
      • End position should be increased by 1
      • Start position should be increased by 1

Exome SNPs - NA12878

  • Currently:
    • Running script to separate our SNP calls and 1KG SNP calls by in-range and out-of-range
    • NOTE: File Dr. Zhang provided uses a slightly inaccurate start position; needs to be incremented by 1 for the residue based coordinate system. End is accurate.

Specific vs. Nonspecific capture

  • For our SNP calls:
    • FOUND THAT 3190/20762 were NONSPECIFIC
    • ~85% specific capture
  • Want to separate false positives from true positives in our SNPs.

Comparison of our SNP calls to 1KG

  • Compared our SNP calls to 1KG
    • Found (out of 20,761 SNPs):
    • 16319 hits (~78.5%)
    • 598 miscalls (~3%)
    • 3844 misses (~18.5%)
  • Need to determine reasons for this
    • Plot of quality and coverage:

NEXT STEPS:

  • Look at IPS data; plot quality and coverage of SNPs.
  • Run bowtie on runs from NA12878 that have high false positives - Done
  • See if there is a pattern; can we separate these false positives out somehow?

NA12878 High False Positive Reads

  • Locations
    • 07282009_HL002, Lanes 4-7
    • 08052009_HL003, Lanes 4-5
  • Storing data on genome-miner:/media/TmpStore1/AG_Scratch/Exome/NA12878
  • Using this sample for validation
    • First step, need to map these reads.
    • Start out with reads on a per experiment basis
      • Merge s_4 through s_7 in HL002, merge s_4 and s_5 in HL003
      • Run Bowtie-SAM script on these merged sets; check results
      • Bowtie-SAM has been run on both HL003 and HL002.
  • Next Steps:
    • Check both of these samples against dbSNP
    • Check both of these samples against 1KG
    • Is there anything similar among the false positives?