Dinh/Dinh 2012/NOTES/2012-2-10
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Tech Rep 9[edit]
- SimulationResults_2082012 finished running
- Initial analysis using R:
> A = read.table("SimulationResults_2082012", header=FALSE) > cor(abs(A$V13-0.5), A$V14/200) NOTE: column V13 is the estimated mean methylation fraction NOTE: column V14 is the sum of the simulated standard deviation (there are 200 of them) correlation of mean methylation fraction and standard deviation is : Pearson's r = -0.703 (the farther from 0.5, the lower the standard deviation)
Bisulfite Patch PCR[edit]
- Current status of the program:
- Objectives:
1) enzyme(s) that can make the best pieces (scored by #of target CpGs)
- Procedure:
0) Set of enzyme(s) 1) Take all possible cut-sites wSNP and woSNP 2) Obtain "usable" pieces from cut-sites(woSNP) "usable" pieces are: 100-200bp and contain >=1 target CpGs and does not contain cut-sites(wSNP) Note that "unusable" pieces may contain cut-sites(wSNP). And all pieces considered are by cut-sites(woSNP) 4) Count only #of target CpGs which are in "usable" pieces 5) Keep enzyme(s) set which gives the highest #of target CpGs
- Finer details:
We obtain cut-sites(wSNP) by enumerating possible every word(of lengths 3-29) in the target region with up to 3 SNPs.
- Michelle incorporated the code to build cut-sites(wSNP).