Athurva Gore/LabNotes/2009-8-28

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Navigation[edit]

To Do[edit]

  • Forms for Tech Transfer Office
  • Invoice for Zymo

Removing Reads with Multiple SNPS[edit]

DF699[edit]

  • Took results from removal of reads w/SNPs in the last 15 bp
  • Removed reads that had more than one SNP.
  • 9386 hits, 1103 misses
  • Don't do any better than just removing those with SNPs in the last 15 bp.
    • Probably not the approach to take.

Remaining options[edit]

  • Considered:
    • Removing reads w/multiple SNPs
    • Removing reads w/SNPs near the end (removes many bad SNPs, but also some good SNPs)
    • Trimming reads w/SNPs near the end (removes many bad SNPs as well; retains more good and bad though)
  • Still remaining:
    • Reducing quality score of SNPs - probably won't see any better results than above
    • New Idea: Split reads into two sections; first 25, last 15?
  • For now, we will go with removing reads with SNPs near the end

IPS and Cancer[edit]

  • For Proposal, preliminary data is needed of the difference between DF699 and fibroblast.
    • Want this data to be high quality
  • Started with results that removed reads w/ SNPs withing 15 bp of the end
  • Then ran pileup2variantsPair with min coverage of 8 and min quality of 20.
  • Used a chi-squared test and removed SNPs that scored lower than 6.
  • Found:
    • 193 SNPs
    • 145 not at dbSNP locations (the above 48 are probably just miscalls in one case due to biased capture)
      • 128 Loss-of-Heterozygosity
      • 13 Gain-of-Heterozygosity
      • 4 Doubles
    • If these GOH mutations are investigated, only 5 are nonsynonymous
      • 3 of these appear in the COSMIC set
    • Decided to check both LOH and GOH mutations to see if any are valid.
      • SIFT: Does it report ref/call? Or does it report in same order?
      • None are classified as purely damaging by SIFT; one is damaging but with low confidence
  • Need to investigate data itself, check over SNPs.
  • Decided to compare to a filter where SNPs had a minimum coverage of 4 instead
    • Will pass just GOH to SIFT, check to see if analysis for presentation was correct