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==Data analysis of recent Solexa runs== ===Criteria for ASE=== * Heterozygous SNPs: gDNA MAF < 0.15 (false positive rate=8/541=1.5%) * cDNA MAF<0.4; * Chi-square > 6.64 (p=0.01, df =1); * Three categories: #Balanced; #Imbalanced; #Uncertain; * 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=== {| {{table}} | align="center" style="background:#f0f0f0;"|'''ID''' | align="center" style="background:#f0f0f0;"|'''Agilent Lib''' | align="center" style="background:#f0f0f0;"|'''Probe prep''' | align="center" style="background:#f0f0f0;"|'''Sample''' | align="center" style="background:#f0f0f0;"|'''Capturing reaction''' | align="center" style="background:#f0f0f0;"|'''Sample shipped''' | align="center" style="background:#f0f0f0;"|'''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) |- | |}
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