%%bash
find zr2096_*R1* \
| xargs basename -s _s1_R1_val_1.fq.gz | xargs -I{} /Applications/bioinfo/Bismark_v0.19.0/bismark \
--path_to_bowtie /Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64 \
--genome /Volumes/Serine/wd/18-03-15/genome \
--score_min L,0,-1.2 \
-u 1000000 \
-p 4 \
--non_directional \
-1 {}_s1_R1_val_1.fq.gz \
-2 {}_s1_R2_val_2.fq.gz \
2> bismark.err

%%bash
/Applications/bioinfo/Bismark_v0.19.0/deduplicate_bismark \
--bam -p \
*.bam \
2> dedup.err

%%bash
find *deduplicated.bam \
| xargs basename -s _s1_R1_val_1_bismark_bt2_pe.deduplicated.bam | xargs -I{} /Applications/bioinfo/samtools-1.3.1/samtools \
sort {}_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam -o {}_dedup.sorted.bam

library(methylKit)

file.list_a=list('zr2096_1_dedup.sorted.bam',
 'zr2096_2_dedup.sorted.bam',
  'zr2096_3_dedup.sorted.bam',
  'zr2096_4_dedup.sorted.bam',
  'zr2096_5_dedup.sorted.bam',
  'zr2096_6_dedup.sorted.bam',
  'zr2096_6_dedup.sorted.bam',
  'zr2096_8_dedup.sorted.bam',
  'zr2096_9_dedup.sorted.bam',
  'zr2096_10_dedup.sorted.bam'
  )

myobj2 = processBismarkAln(location = file.list_a, sample.id = list("1","2","3","4","5","6","7","8","9","10"), assembly = "v3", read.context="CpG", mincov=1, treatment = c(0,0,0,0,0,1,1,1,1,1))

getMethylationStats(myobj2[[1]],plot=FALSE,both.strands=FALSE)

getMethylationStats(myobj2[[1]],plot=TRUE,both.strands=FALSE)

getCoverageStats(myobj2[[4]],plot=TRUE,both.strands=FALSE)

meth=unite(myobj2)

getCorrelation(meth,plot=TRUE)

clusterSamples(meth, dist="correlation", method="ward", plot=TRUE)

getCorrelation(meth,plot=TRUE)


clusterSamples(meth, dist="correlation", method="ward", plot=TRUE)



hc = clusterSamples(meth, dist="correlation", method="ward", plot=FALSE)

PCASamples(meth, screeplot=TRUE)

PCASamples(meth)

myDiff=calculateDiffMeth(meth)

myDiff25p=getMethylDiff(myDiff,difference=25,qvalue=0.01)

myDiff50p <- getMethylDiff(myDiff,difference=50,qvalue=0.01)

write.table(myDiff50p, file = "analyses/myDiff50p.tab")

View(myDiff50p)

install.packages("devtools")

library(devtools)

source("https://bioconductor.org/biocLite.R")
biocLite("methylKit")

install_github("al2na/methylKit", build_vignettes=FALSE, 
               repos=BiocInstaller::biocinstallRepos(),
               dependencies=TRUE)


library(methylKit)