DNA甲基化:DNA甲基化为DNA化学修饰的一种形式,能在不改变DNA序列的前提下,改变遗传表现。为表观遗传编码的一部分,是一种外遗传机制。DNA甲基化过程会使甲基添加到DNA分子上,例如在胞嘧啶环的5’碳上:这种5’方向的DNA甲基化方式可见于所有脊椎动物。 在人类细胞内,大约有1%的DNA碱基受到了甲基化。
gzip -dc A.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz > A.1_bismark_bt2_pe.deduplicated.CX_report.txt perl BismarkCX2methykit.pl A.1_bismark_bt2_pe.deduplicated.CX_report.txt #准备注释需要的bed文件(格式12) convert2bed -i gtf < out.gtf > out6.bed grep 'exon' out6.bed > aa && mv aa out6.bed python3 bed6Tobed12.py out6.bed > out12.bed#bed6Tobed12.py #methylKit安装及使用 if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("methylKit") library(methylKit) file.list = list("A.CG_methykit.txt","B.CG_methykit.txt","C.CG_methykit.txt","D.CG_methykit.txt","E.CG_methykit.txt","F.CG_methykit.txt","G.CG_methykit.txt","H.CG_methykit.txt","I.CG_methykit.txt") myobjDB=methRead(file.list, sample.id=list("Control_1","Control_2","Control_3","Single_1","Single_2","Single_3","Multiple_1","Multiple_2","Multiple_3"), assembly="HZGC", treatment=c(0,0,0,1,1,1,2,2,2), context="CpG", mincov = 10, dbtype = "tabix", dbdir = "methylDB", ) filtered.myobj=filterByCoverage(myobjDB,lo.count=10,lo.perc=NULL, hi.count=NULL,hi.perc=99.9) meth=unite(filtered.myobj, destrand=FALSE) pdf("Correlation.pdf") getCorrelation(meth,plot=TRUE) dev.off() pdf("clusterSamples.pdf") clusterSamples(meth, dist="correlation", method="ward", plot=TRUE) dev.off() pdf("PCAscreeplot.pdf") PCASamples(meth, screeplot=TRUE) dev.off() pdf("PCAcluster.pdf") PCASamples(meth) dev.off() tiles=tileMethylCounts(filtered.myobj,win.size=1000,step.size=1000) meth=unite(tiles, destrand=FALSE) myDiff=calculateDiffMeth(meth,num.cores=10) diffMethPerChr(myDiff,plot=FALSE,qvalue.cutoff=0.01, meth.cutoff=25) myDiff25p.hyper=getMethylDiff(myDiff,difference=25,qvalue=0.01,type="hyper") myDiff25p.hypo=getMethylDiff(myDiff,difference=25,qvalue=0.01,type="hypo") myDiff25p=getMethylDiff(myDiff,difference=25,qvalue=0.01) diffMethPerChr(myDiff,plot=FALSE,qvalue.cutoff=0.01, meth.cutoff=25) save.image("MS_M_S.RData") Diffdataframe=getData(myDiff25p) write.table(Diffdataframe, file="Diffdataframe.xls", sep="\t", quote=F, row.names=T, col.names=T)
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