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=HL110 read 2 resynthesis= *Using Read 2 Cluster Resynthesis Kit *Thaw content of kit on ice *Prepare HP3 (#19) **2.85 mL PW1 + 150 ul of 2 N NaOH *Prepare HP2 (#16) **Content is 3 mL **Add: 15 ul of each: SolSeqV6.3.2r, N2RevSeq2, and Nextera2 =Family background substraction with UCLA samples= *The ANOVA is a generalization of the two sample t-test to find out whether multiple populations have equal means **If different families have different population means at a CpG site then it is influenced by family background *The ANOVA test requires a normality assumption, where the individual in each group is picked from a normal distribution **This is not true since there are affected/unaffected members in each family so it may be skewed. *The Kruskal-Wallis test can be applied to test where we test the null hypothesis that the samples come from populations such that the probability of a random observation from one group is greater than a random observation from another group is 0.5 **Be careful using this test when the different groups have different shapes or variances. *The p value of the Kruskal-Wallis test follows a chi-square distribution, with degrees of freedom = the number of groups minus 1. **It does not follow chi-square if N in each group is < 5. *Script to perform test: [[File:cpgMatrixKrushalWallis.txt]] **Used only families with at least 5 members as groups to find the statistics. **Filter out sites where the p-value < 0.10 ==Hierarchical clustering== Example of how the h-clust were each generated > A =read.table("sites_KW_signif0.10", header=TRUE, row.names=1) > A$STDEV=NULL > A$KW_pvalue=NULL > A$min_RD=NULL > A$mean_RD=NULL > B=as.matrix(A) > dissim=1-abs(cor(B,method="pearson", use="pairwise.complete.obs")) > nrow(A) > distance=as.dist(dissim) > plot(hclust(distance, method="average"), main="Kruskal-Wallis significant sites, n=") > pdf("Kruskal-Wallis significant sites 0.10") > plot(hclust(distance, method="average"), main="Kruskal-Wallis significant sites, n=") > dev.off() *[[File:Kruskal-Wallis-family-substraction-UCLA.pdf]] =Sample identity check= *Took *.snp file generated by the mapping pipeline *Used bisSnpFilterHg19.pl to filter the SNPs *Count homozygous [ATGC] calls and heterozygous [^AGTC] calls for chromosome X {| {{table}} border=1 | align="center" style="background:#f0f0f0;"|'''Comments''' | align="center" style="background:#f0f0f0;"|'''Data_ID''' | align="center" style="background:#f0f0f0;"|'''Number of heterozygous X SNP''' | align="center" style="background:#f0f0f0;"|'''Number of homozygous X SNP''' | align="center" style="background:#f0f0f0;"|'''%het''' | align="center" style="background:#f0f0f0;"|'''%hom''' | align="center" style="background:#f0f0f0;"|'''Sample_ID''' | align="center" style="background:#f0f0f0;"|'''Sex''' |- | Mislabeled as female ||GK0210-002||2||62||3%||97%||GK0210-002||Female |- | Mislabeled as female ||GK0277-002||2||45||4%||96%||GK0277-002||Female |- | ||GK0178-003||57||70||45%||55%||GK0178-003||Female |- | ||GK0100-003||47||48||49%||51%||GK0100-003||Female |- | ||GK0050-003||54||55||50%||50%||GK0050-003||Female |- | ||GK0050-002||54||54||50%||50%||GK0050-002||Female |- | ||GK0100-002||67||65||51%||49%||GK0100-002||Female |- | ||GK0277-004||58||56||51%||49%||GK0277-004||Female |- | ||GK0344-003||68||65||51%||49%||GK0344-003||Female |- | ||GK0271-003||70||66||51%||49%||GK0271-003||Female |- | ||GK0359-004||59||54||52%||48%||GK0359-004||Female |- | ||GK0005-002||76||69||52%||48%||GK0005-002||Female |- | ||GK0123-005||62||56||53%||47%||GK0123-005||Female |- | ||GK0167-006||56||50||53%||47%||GK0167-006||Female |- | ||GK0122-003||51||45||53%||47%||GK0122-003||Female |- | ||GK0091-003||72||63||53%||47%||GK0091-003||Female |- | ||GK0391-002||54||46||54%||46%||GK0391-002||Female |- | ||GK0271-004||74||62||54%||46%||GK0271-004||Female |- | ||GK0365-002||62||51||55%||45%||GK0365-002||Female |- | ||GK0123-003||64||51||56%||44%||GK0123-003||Female |- | ||GK0241-004||51||40||56%||44%||GK0241-004||Female |- | ||GK0167-003||48||37||56%||44%||GK0167-003||Female |- | ||GK0295-002||55||42||57%||43%||GK0295-002||Female |- | ||GK0396-002||75||57||57%||43%||GK0396-002||Female |- | ||GK0187-002||62||47||57%||43%||GK0187-002||Female |- | ||GK0281-002||59||43||58%||42%||GK0281-002||Female |- | ||GK0027-003||66||46||59%||41%||GK0027-003||Female |- | ||GK0359-003||63||42||60%||40%||GK0359-003||Female |- | ||GK0241-002||76||50||60%||40%||GK0241-002||Female |- | ||GK0290-002||64||42||60%||40%||GK0290-002||Female |- | ||GK0005-004||0||53||0%||100%||GK0005-004||Male |- | ||GK0091-001||0||64||0%||100%||GK0091-001||Male |- | ||GK0123-001||0||56||0%||100%||GK0123-001||Male |- | ||GK0178-004||0||77||0%||100%||GK0178-004||Male |- | ||GK0187-001||0||83||0%||100%||GK0187-001||Male |- | ||GK0277-005||0||62||0%||100%||GK0277-005||Male |- | ||GK0281-001||0||51||0%||100%||GK0281-001||Male |- | ||GK0290-001||0||65||0%||100%||GK0290-001||Male |- | ||GK0290-004||0||60||0%||100%||GK0290-004||Male |- | ||GK0295-003||0||64||0%||100%||GK0295-003||Male |- | ||GK0344-002||0||70||0%||100%||GK0344-002||Male |- | ||GK0344-004||0||53||0%||100%||GK0344-004||Male |- | ||GK0391-001||0||70||0%||100%||GK0391-001||Male |- | ||GK0005-001||1||80||1%||99%||GK0005-001||Male |- | ||GK0271-001||1||79||1%||99%||GK0271-001||Male |- | ||GK0365-003||1||79||1%||99%||GK0365-003||Male |- | ||GK0391-003||1||77||1%||99%||GK0391-003||Male |- | ||GK0210-003||1||75||1%||99%||GK0210-003||Male |- | ||GK0277-003||1||72||1%||99%||GK0277-003||Male |- | ||GK0123-004||1||71||1%||99%||GK0123-004||Male |- | ||GK0344-001||1||70||1%||99%||GK0344-001||Male |- | ||GK0396-003||1||70||1%||99%||GK0396-003||Male |- | ||GK0187-004||1||69||1%||99%||GK0187-004||Male |- | ||GK0100-001||1||67||1%||99%||GK0100-001||Male |- | ||GK0281-003||1||65||2%||98%||GK0281-003||Male |- | ||GK0100-006||1||64||2%||98%||GK0100-006||Male |- | ||GK0122-001||1||63||2%||98%||GK0122-001||Male |- | ||GK0295-004||1||63||2%||98%||GK0295-004||Male |- | ||GK0396-001||1||62||2%||98%||GK0396-001||Male |- | ||GK0100-004||1||61||2%||98%||GK0100-004||Male |- | ||GK0178-002||1||60||2%||98%||GK0178-002||Male |- | ||GK0359-006||1||60||2%||98%||GK0359-006||Male |- | ||GK0167-002||1||59||2%||98%||GK0167-002||Male |- | ||GK0241-005||1||59||2%||98%||GK0241-005||Male |- | ||GK0122-004||1||56||2%||98%||GK0122-004||Male |- | ||GK0365-001||1||56||2%||98%||GK0365-001||Male |- | ||GK0359-001||1||54||2%||98%||GK0359-001||Male |- | ||GK0005-003||1||51||2%||98%||GK0005-003||Male |- | #1||GK0123-002||1||49||2%||98%||GK0123-002||Male |- | ||GK0167-001||1||48||2%||98%||GK0167-001||Male |- | ||GK0091-002||2||92||2%||98%||GK0091-002||Male |- | ||GK0241-003||1||46||2%||98%||GK0241-003||Male |- | ||GK0277-001||1||42||2%||98%||GK0277-001||Male |- | ||GK0091-004||2||82||2%||98%||GK0091-004||Male |- | ||GK0027-004||2||79||2%||98%||GK0027-004||Male |- | ||GK0178-001||2||77||3%||97%||GK0178-001||Male |- | ||GK0210-004||2||76||3%||97%||GK0210-004||Male |- | ||GK0391-004||2||76||3%||97%||GK0391-004||Male |- | ||GK0295-001||2||74||3%||97%||GK0295-001||Male |- | ||GK0271-002||2||70||3%||97%||GK0271-002||Male |- | ||GK0290-003||2||68||3%||97%||GK0290-003||Male |- | ||GK0167-004||2||67||3%||97%||GK0167-004||Male |- | ||GK0365-004||2||65||3%||97%||GK0365-004||Male |- | ||GK0271-005||2||64||3%||97%||GK0271-005||Male |- | ||GK0241-001||2||60||3%||97%||GK0241-001||Male |- | ||GK0359-002||2||58||3%||97%||GK0359-002||Male |- | ||GK0027-001||2||56||3%||97%||GK0027-001||Male |- | ||GK0050-004||3||66||4%||96%||GK0050-004||Male |- | #2||GK0123-002||2||44||4%||96%||GK0123-002||Male |- | ||GK0027-002||3||63||5%||95%||GK0027-002||Male |- | ||GK0122-002||3||60||5%||95%||GK0122-002||Male |- | ||GK0187-003||3||57||5%||95%||GK0187-003||Male |- | ||GK0050-001||4||63||6%||94%||GK0050-001||Male |- | Mislabeled as male ||GK0396-004||62||70||47%||53%||GK0396-004||Male |- | Mislabeled as male ||GK0210-001||63||59||52%||48%||GK0210-001||Male |- | Mislabeled as male ||GK0050-005||63||57||53%||48%||GK0050-005||Male |- | No data||GK0281-004||XX||XX||XX||XX||GK0281-004||Male |}
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