Kun:LabNotes/ASE/2008-2-1

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Data analysis of recent Solexa runs

Criteria for ASE

  1. 1 Heterozygous SNPs: gDNA MAF < 0.15 (false positive rate=8/541=1.5%)
  2. 2 cDNA MAF<0.4;
  3. 3 Chi-square > 6.64 (p=0.01, df =1);
  4. 4 Three categories:
  • Balanced;
  • Imbalanced;
  • Uncertain;
  1. 5 Three level ofs confidence
  • Consistent: at least two SNPs with the consistent pattern.
  • Probably: only one SNPs in a gene.
  • Conflicting: two or more SNPs showing conflicting patterns.

Summary of Solexa runs

ID Agilent Lib Probe prep Sample Capturing reaction Sample shipped Solexa run
1 CES22k ?? NA10835 gDNA ??, did by Billy 11/8/2007 11/17/2007(good)
2 CES22k ?? NA20431 gDNA ??, did by Billy 11/8/2007 11/17/2007(good)
3 CES22k ?? GM20431 cDNA ??, did by Billy 11/8/2007 11/17/2007(good)
4 CES22k ?? GM20431 cDNA ??, did by Billy 11/8/2007 11/17/2007(good)
5 CES22k, #3,#4,#5 pooled 11/9/2007 NA20431 gDNA (347ng/ul) 11/20/2007 11/26/2007 11/29/2007 (good)
6 CES22k, #3,#4,#5 pooled 11/9/2007 GM20431 cDNA (121ng/ul) 11/20/2007 11/26/2007 11/29/2007 (good)
7 CES22k, #3,#4,#5 pooled 11/9/2007 GC1F cDNA 11/20/2007 11/26/2007 11/29/2007 (good)
8 CES22k, #3,#4,#5 pooled 11/9/2007 GC1EP cDNA 11/20/2007 11/26/2007 11/29/2007 (good)
9 CES22k ?? GC1F cDNA ??, did by Billy 11/8/2007 12/05/2007(good)
10 CES22k ?? GC1EP cDNA ??, did by Billy 11/8/2007 12/05/2007(good)
11 eSNP84k 11/6/2007 Hues6 gDNA 11/11/2007 11/14/2007 12/05/2007(good)
12 eSNP84k 11/6/2007 Hues6 cDNA 11/11/2007 11/14/2007 12/05/2007(good)
13 CES22k, #5, 10783810008 12/6/2007 127nM NA20431 gDNA (347ng/ul) 12/9/2007 12/17/2007 12/19/2007 (failed), 01/15/2008 (good)
14 CES22k, #5, 10783810008 12/6/2007 127nM GM20431 cDNA (121ng/ul) 12/9/2007 12/17/2007 12/19/2007 (failed), 01/15/2008 (good)
15 CES22k, #5, 10783810008 12/6/2007 127nM GC1F cDNA (48ng/ul) 12/9/2007 12/17/2007 12/19/2007 (failed)
16 CES22k, #5, 10783810008 12/6/2007 127nM GC1EP cDNA (52ng/ul) 12/9/2007 12/17/2007 12/19/2007 (failed)
17 CES22k, #5, 10783810008 1/12/2008 NA20431 gDNA (347ng/ul) 1/13/2008 1/17/2008 01/19/2008 (good)
18 CES22k, #5, 10783810008 1/12/2008 GM20431 cDNA (121ng/ul) 1/13/2008 1/17/2008 01/19/2008 (good)
19 CES22k, #5, 10783810008 1/12/2008 GC1F cDNA (57ng/ul) 1/13/2008 1/17/2008 01/19/2008 (good)
20 CES22k, #5, 10783810008 1/12/2008 GC1EP cDNA (114ng/ul) 1/13/2008 1/17/2008 01/19/2008 (good)