diff --git a/comparePeaks.R b/comparePeaks.R
deleted file mode 100755
index 9923fbd85519282443daf89b37fdc408bb68fb5a..0000000000000000000000000000000000000000
--- a/comparePeaks.R
+++ /dev/null
@@ -1,451 +0,0 @@
-library(liftOver)
-library(ChIPpeakAnno)
-
-###################################################################################################
-###################################### COMPARING PEAKS ############################################
-###################################################################################################
-
-## All peaks
-system("less enhancers/dunnart_enhancer_peaks.narrowPeak | awk '{print $1,$2,$3}' > dunnart.enhancer_peaks_coord.bed",intern=TRUE)
-system("less promoters/clustered/dunnart.clustered.narrowPeak | awk '{print $1,$2,$3}' > promoters/clustered/dunnart.promoter_peaks_coord.bed",intern=TRUE)
-
-system("liftOver enhancers/dunnart.enhancer_peaks_coord.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain dunnart.enhancer_smiCraTOmm10.bed enhancer_smiCraTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver promoters/clustered/dunnart.promoter_peaks_coord.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain dunnart.promoter_smiCraTOmm10.bed promoter_smiCraTOmm10_unmapped.bed",intern=TRUE)
-# enhancer = 437 peaks
-# promoter = 48 peaks
-
-
-## LiftOver peaks allowing for multiple matches
-## Minimum target size is 50bp
-## Minimum query size is 50bp
-
-system("liftOver -bedPlus=3 -multiple -minChainT=100 -minChainQ=100 enhancers/dunnart_enhancer_peaks.narrowPeak ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/dunnart.enhancer_smiCraTOmm10.bed enhancers/enhancer_smiCraTOmm10_unmapped.bed",intern=TRUE)
-## 29347
-system("liftOver -bedPlus=3 -multiple -minChainT=100 -minChainQ=100 promoters/clustered/dunnart.clustered.narrowPeak ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/dunnart.promoter_smiCraTOmm10.bed promoters/clustered/promoter_smiCraTOmm10_unmapped.bed",intern=TRUE)
-## 20191
-
-# Import output files
-enh = fread("enhancers/dunnart.enhancer_smiCraTOmm10.bed")
-prom = fread("promoters/clustered/dunnart.promoter_smiCraTOmm10.bed")
-data = list(enh, prom)
-names(data) = c("enhancers", "promoters")
-data = Map(mutate, data, cre = names(data))
-data = lapply(data, function(x) x[order(V4),])
-data = lapply(data, function(x) x=x[,width:=V3-V2])
-data = rbindlist(data,)
-
-
-###################################################################################################
-################################### EXTRACT PEAK SUMMITS ########################################
-###################################################################################################
-
-# make list of peaks enhancer and promoter groups
-system("less enhancers/dunnart_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}' | sort > enhancers/enhancer_peak_IDs.txt", intern=TRUE)
-system("less promoters/clustered/dunnart.clustered.narrowPeak | awk -F '\t' '{print $4}' | sort > promoters/clustered/promoter_peak_IDs.txt", intern=TRUE)
-
-system("cat /data/projects/punim0586/lecook/chipseq-pipeline/dunnart/results_10M/macs2/H3K4me3_pooled_macs2_summits.bed /data/projects/punim0586/lecook/chipseq-pipeline/dunnart/results_10M/macs2/H3K27ac_pooled_macs2_summits.bed > H3K4me3_H3K27ac_combinedSummits.bed", intern=TRUE)
-
-system("less E10.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}' > E10.5_enhancer_peaks_IDs.txt",intern=TRUE)
-system("less E11.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}' > E11.5_enhancer_peaks_IDs.txt",intern=TRUE)
-system("less E12.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}' > E12.5_enhancer_peaks_IDs.txt",intern=TRUE)
-system("less E13.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}' > E13.5_enhancer_peaks_IDs.txt",intern=TRUE)
-system("less E14.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}' > E14.5_enhancer_peaks_IDs.txt",intern=TRUE)
-system("less E15.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}' > E15.5_enhancer_peaks_IDs.txt",intern=TRUE)
-
-system("less E10.5.clustered.narrowPeak | awk -F '\t' '{print $4}' > promoters/clustered/E10.5_promoter_peaks_IDs.txt",intern=TRUE)
-system("less E11.5.clustered.narrowPeak | awk -F '\t' '{print $4}' > promoters/clustered/E11.5_promoter_peaks_IDs.txt",intern=TRUE)
-system("less E12.5.clustered.narrowPeak | awk -F '\t' '{print $4}' > promoters/clustered/E12.5_promoter_peaks_IDs.txt",intern=TRUE)
-system("less E13.5.clustered.narrowPeak | awk -F '\t' '{print $4}' > promoters/clustered/E13.5_promoter_peaks_IDs.txt",intern=TRUE)
-system("less E14.5.clustered.narrowPeak | awk -F '\t' '{print $4}' > promoters/clustered/E14.5_promoter_peaks_IDs.txt",intern=TRUE)
-system("less E15.5.clustered.narrowPeak | awk -F '\t' '{print $4}' > promoters/clustered/E15.5_promoter_peaks_IDs.txt",intern=TRUE)
-
-setwd("/data/projects/punim0586/lecook/chipseq-pipeline/mouse/results_10M/macs2")
-system("cat E10.5_H3K27ac.pooled.macs2_summits.bed E10.5_H3K4me3.pooled.macs2_summits.bed > ../../../cross_species/peakAnnotation/consensus/E10.5_H3K27ac_H3K4me3.pooled.macs2_summits.bed", intern=TRUE)
-system("cat E11.5_H3K27ac.pooled.macs2_summits.bed E11.5_H3K4me3.pooled.macs2_summits.bed > ../../../cross_species/peakAnnotation/consensus/E11.5_H3K27ac_H3K4me3.pooled.macs2_summits.bed", intern=TRUE)
-system("cat E12.5_H3K27ac.pooled.macs2_summits.bed E12.5_H3K4me3.pooled.macs2_summits.bed > ../../../cross_species/peakAnnotation/consensus/E12.5_H3K27ac_H3K4me3.pooled.macs2_summits.bed", intern=TRUE)
-system("cat E13.5_H3K27ac.pooled.macs2_summits.bed E13.5_H3K4me3.pooled.macs2_summits.bed > ../../../cross_species/peakAnnotation/consensus/E13.5_H3K27ac_H3K4me3.pooled.macs2_summits.bed", intern=TRUE)
-system("cat E14.5_H3K27ac.pooled.macs2_summits.bed E14.5_H3K4me3.pooled.macs2_summits.bed > ../../../cross_species/peakAnnotation/consensus/E14.5_H3K27ac_H3K4me3.pooled.macs2_summits.bed", intern=TRUE)
-system("cat E15.5_H3K27ac.pooled.macs2_summits.bed E15.5_H3K4me3.pooled.macs2_summits.bed > ../../../cross_species/peakAnnotation/consensus/E15.5_H3K27ac_H3K4me3.pooled.macs2_summits.bed", intern=TRUE)
-
-# in R extract rows from summits file based on the list of peaks in overlap file for both enhancers and promoters
-## Dunnart
-
-summits <- read.table("H3K4me3_H3K27ac_combinedSummits.bed")
-reps1 <- scan("enhancers/enhancer_peak_IDs.txt", what="", sep="\n")
-reps2 <- scan("promoters/clustered/promoter_peak_IDs.txt", what="", sep="\n")
-enh_summits <- subset(summits, V4 %in% reps1)
-pro_summits <- subset(summits, V4 %in% reps2)
-write.table(enh_summits, "dunnart.enhancer_overlap_summits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-write.table(pro_summits, "dunnart.promoter_overlap_summits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-
-## Mouse
-setwd("/data/projects/punim0586/lecook/chipseq-pipeline/cross_species/peakAnnotation/consensus")
-E10 <- read.table("E10.5_H3K27ac_H3K4me3.pooled.macs2_summits.bed")
-E11<- read.table("E11.5_H3K27ac_H3K4me3.pooled.macs2_summits.bed")
-E12<- read.table("E12.5_H3K27ac_H3K4me3.pooled.macs2_summits.bed")
-E13<- read.table("E13.5_H3K27ac_H3K4me3.pooled.macs2_summits.bed")
-E14<- read.table("E14.5_H3K27ac_H3K4me3.pooled.macs2_summits.bed")
-E15<- read.table("E15.5_H3K27ac_H3K4me3.pooled.macs2_summits.bed")
-
-p10 <- scan("promoters/clustered/E10.5_promoter_peaks_IDs.txt", what="", sep="\n")
-p11 <- scan("promoters/clustered/E11.5_promoter_peaks_IDs.txt", what="", sep="\n")
-p12 <- scan("promoters/clustered/E12.5_promoter_peaks_IDs.txt", what="", sep="\n")
-p13 <- scan("promoters/clustered/E13.5_promoter_peaks_IDs.txt", what="", sep="\n")
-p14 <- scan("promoters/clustered/E14.5_promoter_peaks_IDs.txt", what="", sep="\n")
-p15 <- scan("promoters/clustered/E15.5_promoter_peaks_IDs.txt", what="", sep="\n")
-
-e10 <- scan("enhancers/E10.5_enhancer_peaks_IDs.txt", what="", sep="\n")
-e11 <- scan("enhancers/E11.5_enhancer_peaks_IDs.txt", what="", sep="\n")
-e12 <- scan("enhancers/E12.5_enhancer_peaks_IDs.txt", what="", sep="\n")
-e13 <- scan("enhancers/E13.5_enhancer_peaks_IDs.txt", what="", sep="\n")
-e14 <- scan("enhancers/E14.5_enhancer_peaks_IDs.txt", what="", sep="\n")
-e15 <- scan("enhancers/E15.5_enhancer_peaks_IDs.txt", what="", sep="\n")
-
-write.table(subset(E10, V4 %in% p10), "promoters/clustered/E10_promoter_overlap_summits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-write.table(subset(E11, V4 %in% p11), "promoters/clustered/E11_promoter_overlap_summits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-write.table(subset(E12, V4 %in% p12), "promoters/clustered/E12_promoter_overlap_summits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-write.table(subset(E13, V4 %in% p13), "promoters/clustered/E13_promoter_overlap_summits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-write.table(subset(E14, V4 %in% p14), "promoters/clustered/E14_promoter_overlap_summits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-write.table(subset(E15, V4 %in% p15), "promoters/clustered/E15_promoter_overlap_summits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-
-write.table(subset(E10, V4 %in% e10), "enhancers/E10_enhancer_overlap_summits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-write.table(subset(E11, V4 %in% e11), "enhancers/E11_enhancer_overlap_summits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-write.table(subset(E12, V4 %in% e12), "enhancers/E12_enhancer_overlap_summits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-write.table(subset(E13, V4 %in% e13), "enhancers/E13_enhancer_overlap_summits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-write.table(subset(E14, V4 %in% e14), "enhancers/E14_enhancer_overlap_summits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-write.table(subset(E15, V4 %in% e15), "enhancers/E15_enhancer_overlap_summits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-
-
-# in bash use bedtools to extend the summits 25bp in both directions to have 50bp
-system("bedtools slop -i enhancers/dunnart.enhancer_overlap_summits.bed -b 25 -g smiCra1.chrom.sizes > enhancers/enhancer_overlap_50bpsummits.bed", intern=TRUE)
-system("bedtools slop -i promoters/clustered/dunnart.promoter_overlap_summits.bed -b 25 -g smiCra1.chrom.sizes > promoters/clustered/promoter_overlap_50bpsummits.bed", intern=TRUE)
-
-system("bedtools slop -i enhancers/E10_enhancer_overlap_summits.bed -b 25 -g mm10.chrom.sizes > enhancers/E10_enhancer_overlap_50bpsummits.bed", intern=TRUE)
-system("bedtools slop -i enhancers/E11_enhancer_overlap_summits.bed -b 25 -g mm10.chrom.sizes > enhancers/E11_enhancer_overlap_50bpsummits.bed", intern=TRUE)
-system("bedtools slop -i enhancers/E12_enhancer_overlap_summits.bed -b 25 -g mm10.chrom.sizes > enhancers/E12_enhancer_overlap_50bpsummits.bed", intern=TRUE)
-system("bedtools slop -i enhancers/E13_enhancer_overlap_summits.bed -b 25 -g mm10.chrom.sizes > enhancers/E13_enhancer_overlap_50bpsummits.bed", intern=TRUE)
-system("bedtools slop -i enhancers/E14_enhancer_overlap_summits.bed -b 25 -g mm10.chrom.sizes > enhancers/E14_enhancer_overlap_50bpsummits.bed", intern=TRUE)
-system("bedtools slop -i enhancers/E15_enhancer_overlap_summits.bed -b 25 -g mm10.chrom.sizes > enhancers/E15_enhancer_overlap_50bpsummits.bed", intern=TRUE)
-
-system("bedtools slop -i promoters/clustered/E10_promoter_overlap_summits.bed -b 25 -g mm10.chrom.sizes > promoters/clustered/E10_promoter_overlap_50bpsummits.bed", intern=TRUE)
-system("bedtools slop -i promoters/clustered/E11_promoter_overlap_summits.bed -b 25 -g mm10.chrom.sizes > promoters/clustered/E11_promoter_overlap_50bpsummits.bed", intern=TRUE)
-system("bedtools slop -i promoters/clustered/E12_promoter_overlap_summits.bed -b 25 -g mm10.chrom.sizes > promoters/clustered/E12_promoter_overlap_50bpsummits.bed", intern=TRUE)
-system("bedtools slop -i promoters/clustered/E13_promoter_overlap_summits.bed -b 25 -g mm10.chrom.sizes > promoters/clustered/E13_promoter_overlap_50bpsummits.bed", intern=TRUE)
-system("bedtools slop -i promoters/clustered/E14_promoter_overlap_summits.bed -b 25 -g mm10.chrom.sizes > promoters/clustered/E14_promoter_overlap_50bpsummits.bed", intern=TRUE)
-system("bedtools slop -i promoters/clustered/E15_promoter_overlap_summits.bed -b 25 -g mm10.chrom.sizes > promoters/clustered/E15_promoter_overlap_50bpsummits.bed", intern=TRUE)
-
-
-###################################################################################################
-################################### LIFTOVER PEAK SUMMITS ########################################
-###################################################################################################
-
-#### COMBINED PEAKS - ACTIVE IN BOTH DUNNART AND MOUSE ####
-
-# LiftOver dunnart peaks to mouse genome
-system("liftOver enhancers/enhancer_overlap_50bpsummits.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/enhancer_summit50bp_smiCraTOmm10.bed enhancers/enhancer_summit50bp_smiCraTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver promoters/clustered/promoter_overlap_50bpsummits.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/promoter_summit50bp_smiCraTOmm10.bed promoters/clustered/promoter_summit50bp_smiCraTOmm10_unmapped.bed",intern=TRUE)
-
-## Intersect dunnart CREs with mouse CREs.
-system("bedtools intersect -a promoters/clustered/promoter_summit50bp_smiCraTOmm10.bed -b promoters/clustered/E10.5.clustered.narrowPeak -wo > promoters/clustered/E10.5_promoterOverlapmm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a promoters/clustered/promoter_summit50bp_smiCraTOmm10.bed -b promoters/clustered/E11.5.clustered.narrowPeak -wo > promoters/clustered/E11.5_promoterOverlapmm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a promoters/clustered/promoter_summit50bp_smiCraTOmm10.bed -b promoters/clustered/E12.5.clustered.narrowPeak -wo > promoters/clustered/E12.5_promoterOverlapmm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a promoters/clustered/promoter_summit50bp_smiCraTOmm10.bed -b promoters/clustered/E13.5.clustered.narrowPeak -wo > promoters/clustered/E13.5_promoterOverlapmm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a promoters/clustered/promoter_summit50bp_smiCraTOmm10.bed -b promoters/clustered/E14.5.clustered.narrowPeak -wo > promoters/clustered/E14.5_promoterOverlapmm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a promoters/clustered/promoter_summit50bp_smiCraTOmm10.bed -b promoters/clustered/E15.5.clustered.narrowPeak -wo > promoters/clustered/E15.5_promoterOverlapmm10_50bpsummits.bed",intern=TRUE)
-
-system("bedtools intersect -a enhancer_summit50bp_smiCraTOmm10.bed -b E10.5_enhancer_peaks.narrowPeak -wo > E10.5_enhancerOverlapmm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a enhancer_summit50bp_smiCraTOmm10.bed -b E11.5_enhancer_peaks.narrowPeak -wo > E11.5_enhancerOverlapmm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a enhancer_summit50bp_smiCraTOmm10.bed -b E12.5_enhancer_peaks.narrowPeak -wo > E12.5_enhancerOverlapmm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a enhancer_summit50bp_smiCraTOmm10.bed -b E13.5_enhancer_peaks.narrowPeak -wo > E13.5_enhancerOverlapmm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a enhancer_summit50bp_smiCraTOmm10.bed -b E14.5_enhancer_peaks.narrowPeak -wo > E14.5_enhancerOverlapmm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a enhancer_summit50bp_smiCraTOmm10.bed -b E15.5_enhancer_peaks.narrowPeak -wo > E15.5_enhancerOverlapmm10_50bpsummits.bed",intern=TRUE)
-
-## Lift dunnart peaks back over to the dunnart genome
-system("liftOver -bedPlus=4 promoters/clustered/E10.5_promoterOverlapmm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E10.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed promoters/clustered/E10.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E11.5_promoterOverlapmm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E11.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed promoters/clustered/E11.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E12.5_promoterOverlapmm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E12.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed promoters/clustered/E12.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E13.5_promoterOverlapmm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E13.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed promoters/clustered/E13.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E14.5_promoterOverlapmm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E14.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed promoters/clustered/E14.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E15.5_promoterOverlapmm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E15.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed promoters/clustered/E15.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-
-system("liftOver -bedPlus=4 enhancers/E10.5_enhancerOverlapmm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E10.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed enhancers/E10.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E11.5_enhancerOverlapmm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E11.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed enhancers/E11.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E12.5_enhancerOverlapmm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E12.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed enhancers/E12.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E13.5_enhancerOverlapmm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E13.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed enhancers/E13.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E14.5_enhancerOverlapmm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E14.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed enhancers/E14.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E15.5_enhancerOverlapmm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E15.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed enhancers/E15.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-
-awk 'x[$9]++ == 1 { print $9 " is duplicated"}' E10.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed
-awk 'x[$9]++ == 1 { print $9 " is duplicated"}' E11.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed
-awk 'x[$9]++ == 1 { print $9 " is duplicated"}' E12.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed
-awk 'x[$9]++ == 1 { print $9 " is duplicated"}' E13.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed
-awk 'x[$9]++ == 1 { print $9 " is duplicated"}' E15.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed
-awk 'x[$9]++ == 1 { print $9 " is duplicated"}' E14.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed
-
-# E11.5_H3K27ac.pooled.macs2_peak_13476 is duplicated
-# scaffold00030_pilon_pilon 15206485 15206536 H3K27ac_pooled_macs2_peak_99049 13.07934 chr16 44615130 44617625 E11.5_H3K27ac.pooled.macs2_peak_13476 269 . 10.16625 26.91089 23.58920 1194 51
-# scaffold00030_pilon_pilon 15207575 15207626 H3K27ac_pooled_macs2_peak_99050 28.62918 chr16 44615130 44617625 E11.5_H3K27ac.pooled.macs2_peak_13476 269 . 10.16625 26.91089 23.58920 1194 51
-
-# E11.5_H3K27ac.pooled.macs2_peak_10317 is duplicated
-# scaffold00002_pilon_pilon 130541237 130541288 H3K27ac_pooled_macs2_peak_13645 10.08028 chr14 24825909 24828470 E11.5_H3K27ac.pooled.macs2_peak_10317 372 . 12.48566 37.24145 33.69604 1973 52
-# scaffold00164_pilon_pilon 1438896 1438947 H3K27ac_pooled_macs2_peak_150856 6.25556 chr14 24825909 24828470 E11.5_H3K27ac.pooled.macs2_peak_10317 372 . 12.48566 37.24145 33.69604 1973 51
-
-# E12.5_H3K27ac.pooled.macs2_peak_25988 is duplicated
-# scaffold00030_pilon_pilon 15206485 15206536 H3K27ac_pooled_macs2_peak_99049 13.07934 chr16 44615052 44618395 E12.5_H3K27ac.pooled.macs2_peak_25988 428 . 14.73608 42.88547 39.11777 1216 51
-# scaffold00030_pilon_pilon 15207575 15207626 H3K27ac_pooled_macs2_peak_99050 28.62918 chr16 44615052 44618395 E12.5_H3K27ac.pooled.macs2_peak_25988 428 . 14.73608 42.88547 39.11777 1216 51
-
-# E13.5_H3K27ac.pooled.macs2_peak_35104 is duplicated
-# scaffold00030_pilon_pilon 15206485 15206536 H3K27ac_pooled_macs2_peak_99049 13.07934 chr16 44615114 44617699 E13.5_H3K27ac.pooled.macs2_peak_35104 357 . 9.00248 35.75615 32.52668 1721 51
-# scaffold00030_pilon_pilon 15207575 15207626 H3K27ac_pooled_macs2_peak_99050 28.62918 chr16 44615114 44617699 E13.5_H3K27ac.pooled.macs2_peak_35104 357 . 9.00248 35.75615 32.52668 1721 51
-
-# E13.5_H3K27ac.pooled.macs2_peak_26554 is duplicated
-# scaffold00002_pilon_pilon 130541237 130541288 H3K27ac_pooled_macs2_peak_13645 10.08028 chr14 24825799 24828390 E13.5_H3K27ac.pooled.macs2_peak_26554 324 . 11.76375 32.42406 29.25455 758 52
-# scaffold00164_pilon_pilon 1438896 1438947 H3K27ac_pooled_macs2_peak_150856 6.25556 chr14 24825799 24828390 E13.5_H3K27ac.pooled.macs2_peak_26554 324 . 11.76375 32.42406 29.25455 758 51
-
-# E14.5_H3K27ac.pooled.macs2_peak_24514 is duplicated
-# scaffold00030_pilon_pilon 15206485 15206536 H3K27ac_pooled_macs2_peak_99049 13.07934 chr16 44614943 44618063 E14.5_H3K27ac.pooled.macs2_peak_24514 544 . 11.99538 54.44302 51.09379 1990 51
-# scaffold00030_pilon_pilon 15207575 15207626 H3K27ac_pooled_macs2_peak_99050 28.62918 chr16 44614943 44618063 E14.5_H3K27ac.pooled.macs2_peak_24514 544 . 11.99538 54.44302 51.09379 1990 51
-
-# E14.5_H3K27ac.pooled.macs2_peak_18551 is duplicated
-# scaffold00002_pilon_pilon 130541237 130541288 H3K27ac_pooled_macs2_peak_13645 10.08028 chr14 24825764 24828307 E14.5_H3K27ac.pooled.macs2_peak_18551 263 . 10.19783 26.37918 23.49332 1742 52
-# scaffold00164_pilon_pilon 1438896 1438947 H3K27ac_pooled_macs2_peak_150856 6.25556 chr14 24825764 24828307 E14.5_H3K27ac.pooled.macs2_peak_18551 263 . 10.19783 26.37918 23.49332 1742 51
-
-# E15.5_H3K27ac.pooled.macs2_peak_20587 is duplicated
-# scaffold00030_pilon_pilon 15206485 15206536 H3K27ac_pooled_macs2_peak_99049 13.07934 chr16 44615161 44617589 E15.5_H3K27ac.pooled.macs2_peak_20587 254 . 10.70462 25.49718 22.21071 1155 51
-# scaffold00030_pilon_pilon 15207575 15207626 H3K27ac_pooled_macs2_peak_99050 28.62918 chr16 44615161 44617589 E15.5_H3K27ac.pooled.macs2_peak_20587 254 . 10.70462 25.49718 22.21071 1155 51
-
-awk 'x[$9]++ == 1 { print $9 " is duplicated"}' E10.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed
-awk 'x[$9]++ == 1 { print $9 " is duplicated"}' E11.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed
-awk 'x[$9]++ == 1 { print $9 " is duplicated"}' E12.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed
-awk 'x[$9]++ == 1 { print $9 " is duplicated"}' E13.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed
-awk 'x[$9]++ == 1 { print $9 " is duplicated"}' E15.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed
-awk 'x[$9]++ == 1 { print $9 " is duplicated"}' E14.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed
-
-# E14.5_H3K4me3.pooled.macs2_peak_8068 is duplicated
-# scaffold00098_pilon_pilon 5322430 5322481 H3K4me3_pooled_macs2_peak_110310 7.99621 chr15 8443049 8445832 E14.5_H3K4me3.pooled.macs2_peak_8068 3775 . 73.91695 377.57697 372.49487 1968 51
-# scaffold00200_pilon_pilon 318471 318522 H3K4me3_pooled_macs2_peak_125887 197.97865 chr15 8443049 8445832 E14.5_H3K4me3.pooled.macs2_peak_8068 3775. 73.91695 377.57697 372.49487 1968 53
-
-#### DUNNART SPECIFIC PEAKS - ACTIVE ONLY IN THE DUNNART ####
-## Intersect dunnart CREs with mouse CREs keeping those that DO NOT overlap.
-
-system("bedtools intersect -a promoters/clustered/promoter_summit50bp_smiCraTOmm10.bed -b promoters/clustered/E10.5.clustered.narrowPeak -v > promoters/clustered/E10.5.clustered_dunnart.specific_mm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a promoters/clustered/promoter_summit50bp_smiCraTOmm10.bed -b promoters/clustered/E11.5.clustered.narrowPeak -v > promoters/clustered/E11.5.clustered_dunnart.specific_mm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a promoters/clustered/promoter_summit50bp_smiCraTOmm10.bed -b promoters/clustered/E12.5.clustered.narrowPeak -v > promoters/clustered/E12.5.clustered_dunnart.specific_mm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a promoters/clustered/promoter_summit50bp_smiCraTOmm10.bed -b promoters/clustered/E13.5.clustered.narrowPeak -v > promoters/clustered/E13.5.clustered_dunnart.specific_mm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a promoters/clustered/promoter_summit50bp_smiCraTOmm10.bed -b promoters/clustered/E14.5.clustered.narrowPeak -v > promoters/clustered/E14.5.clustered_dunnart.specific_mm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a promoters/clustered/promoter_summit50bp_smiCraTOmm10.bed -b promoters/clustered/E15.5.clustered.narrowPeak -v > promoters/clustered/E15.5.clustered_dunnart.specific_mm10_50bpsummits.bed",intern=TRUE)
-
-system("bedtools intersect -a enhancers/enhancer_summit50bp_smiCraTOmm10.bed -b enhancers/E10.5_enhancer_peaks.narrowPeak -v > enhancers/E10.5_enhancer_dunnart.specific_mm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a enhancers/enhancer_summit50bp_smiCraTOmm10.bed -b enhancers/E11.5_enhancer_peaks.narrowPeak -v > enhancers/E11.5_enhancer_dunnart.specific_mm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a enhancers/enhancer_summit50bp_smiCraTOmm10.bed -b enhancers/E12.5_enhancer_peaks.narrowPeak -v > enhancers/E12.5_enhancer_dunnart.specific_mm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a enhancers/enhancer_summit50bp_smiCraTOmm10.bed -b enhancers/E13.5_enhancer_peaks.narrowPeak -v > enhancers/E13.5_enhancer_dunnart.specific_mm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a enhancers/enhancer_summit50bp_smiCraTOmm10.bed -b enhancers/E14.5_enhancer_peaks.narrowPeak -v > enhancers/E14.5_enhancer_dunnart.specific_mm10_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a enhancers/enhancer_summit50bp_smiCraTOmm10.bed -b enhancers/E15.5_enhancer_peaks.narrowPeak -v > enhancers/E15.5_enhancer_dunnart.specific_mm10_50bpsummits.bed",intern=TRUE)
-
-## Lift dunnart-specific peaks back over to the dunnart genome
-system("liftOver -bedPlus=4 promoters/clustered/E10.5.clustered_dunnart.specific_mm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E10.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed promoters/clustered/E10.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E11.5.clustered_dunnart.specific_mm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E11.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed promoters/clustered/E11.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E12.5.clustered_dunnart.specific_mm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E12.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed promoters/clustered/E12.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E13.5.clustered_dunnart.specific_mm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E13.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed promoters/clustered/E13.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E14.5.clustered_dunnart.specific_mm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E14.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed promoters/clustered/E14.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E15.5.clustered_dunnart.specific_mm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E15.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed promoters/clustered/E15.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-
-system("liftOver -bedPlus=4 enhancers/E10.5_enhancer_dunnart.specific_mm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E10.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed enhancers/E10.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E11.5_enhancer_dunnart.specific_mm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E11.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed enhancers/E11.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E12.5_enhancer_dunnart.specific_mm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E12.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed enhancers/E12.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E13.5_enhancer_dunnart.specific_mm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E13.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed enhancers/E13.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E14.5_enhancer_dunnart.specific_mm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E14.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed enhancers/E14.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E15.5_enhancer_dunnart.specific_mm10_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E15.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed enhancers/E15.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_unmapped.bed",intern=TRUE)
-
-
-#### MOUSE SPECIFIC PEAKS - ACTIVE ONLY IN THE MOUSE ####
-
-# LiftOver mouse peaks to dunnart genome
-system("liftOver enhancers/E10_enhancer_overlap_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E10_enhancer_summit50bp_mm10TOsmiCra.bed enhancers/E10_enhancer_summit50bp_mm10TOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver enhancers/E11_enhancer_overlap_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E11_enhancer_summit50bp_mm10TOsmiCra.bed enhancers/E11_enhancer_summit50bp_mm10TOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver enhancers/E12_enhancer_overlap_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E12_enhancer_summit50bp_mm10TOsmiCra.bed enhancers/E12_enhancer_summit50bp_mm10TOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver enhancers/E13_enhancer_overlap_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E13_enhancer_summit50bp_mm10TOsmiCra.bed enhancers/E13_enhancer_summit50bp_mm10TOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver enhancers/E14_enhancer_overlap_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E14_enhancer_summit50bp_mm10TOsmiCra.bed enhancers/E14_enhancer_summit50bp_mm10TOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver enhancers/E15_enhancer_overlap_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E15_enhancer_summit50bp_mm10TOsmiCra.bed enhancers/E15_enhancer_summit50bp_mm10TOsmiCra_unmapped.bed",intern=TRUE)
-
-system("liftOver promoters/clustered/E10_promoter_overlap_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E10_promoter_summit50bp_mm10TOsmiCra.bed promoters/clustered/E10_promoter_summit50bp_mm10TOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver promoters/clustered/E11_promoter_overlap_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E11_promoter_summit50bp_mm10TOsmiCra.bed promoters/clustered/E11_promoter_summit50bp_mm10TOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver promoters/clustered/E12_promoter_overlap_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E12_promoter_summit50bp_mm10TOsmiCra.bed promoters/clustered/E12_promoter_summit50bp_mm10TOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver promoters/clustered/E13_promoter_overlap_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E13_promoter_summit50bp_mm10TOsmiCra.bed promoters/clustered/E13_promoter_summit50bp_mm10TOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver promoters/clustered/E14_promoter_overlap_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E14_promoter_summit50bp_mm10TOsmiCra.bed promoters/clustered/E14_promoter_summit50bp_mm10TOsmiCra_unmapped.bed",intern=TRUE)
-system("liftOver promoters/clustered/E15_promoter_overlap_50bpsummits.bed ../mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E15_promoter_summit50bp_mm10TOsmiCra.bed promoters/clustered/E15_promoter_summit50bp_mm10TOsmiCra_unmapped.bed",intern=TRUE)
-
-## Intersect dunnart CREs with mouse CREs keeping those that DO NOT overlap.
-system("bedtools intersect -a promoters/clustered/E10_promoter_summit50bp_mm10TOsmiCra.bed -b promoters/clustered/dunnart.clustered.narrowPeak -v > promoters/clustered/E10.5_promoter_mouse.specific_smiCra_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a promoters/clustered/E11_promoter_summit50bp_mm10TOsmiCra.bed -b promoters/clustered/dunnart.clustered.narrowPeak -v > promoters/clustered/E11.5_promoter_mouse.specific_smiCra_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a promoters/clustered/E12_promoter_summit50bp_mm10TOsmiCra.bed -b promoters/clustered/dunnart.clustered.narrowPeak -v > promoters/clustered/E12.5_promoter_mouse.specific_smiCra_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a promoters/clustered/E13_promoter_summit50bp_mm10TOsmiCra.bed -b promoters/clustered/dunnart.clustered.narrowPeak -v > promoters/clustered/E13.5_promoter_mouse.specific_smiCra_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a promoters/clustered/E14_promoter_summit50bp_mm10TOsmiCra.bed -b promoters/clustered/dunnart.clustered.narrowPeak -v > promoters/clustered/E14.5_promoter_mouse.specific_smiCra_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a promoters/clustered/E15_promoter_summit50bp_mm10TOsmiCra.bed -b promoters/clustered/dunnart.clustered.narrowPeak -v > promoters/clustered/E15.5_promoter_mouse.specific_smiCra_50bpsummits.bed",intern=TRUE)
-
-system("bedtools intersect -a enhancers/E10_enhancer_summit50bp_mm10TOsmiCra.bed -b enhancers/dunnart_enhancer_peaks.narrowPeak -v > enhancers/E10.5_enhancer_mouse.specific_smiCra_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a enhancers/E11_enhancer_summit50bp_mm10TOsmiCra.bed -b enhancers/dunnart_enhancer_peaks.narrowPeak -v > enhancers/E11.5_enhancer_mouse.specific_smiCra_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a enhancers/E12_enhancer_summit50bp_mm10TOsmiCra.bed -b enhancers/dunnart_enhancer_peaks.narrowPeak -v > enhancers/E12.5_enhancer_mouse.specific_smiCra_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a enhancers/E13_enhancer_summit50bp_mm10TOsmiCra.bed -b enhancers/dunnart_enhancer_peaks.narrowPeak -v > enhancers/E13.5_enhancer_mouse.specific_smiCra_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a enhancers/E14_enhancer_summit50bp_mm10TOsmiCra.bed -b enhancers/dunnart_enhancer_peaks.narrowPeak -v > enhancers/E14.5_enhancer_mouse.specific_smiCra_50bpsummits.bed",intern=TRUE)
-system("bedtools intersect -a enhancers/E15_enhancer_summit50bp_mm10TOsmiCra.bed -b enhancers/dunnart_enhancer_peaks.narrowPeak -v > enhancers/E15.5_enhancer_mouse.specific_smiCra_50bpsummits.bed",intern=TRUE)
-
-## Lift mouse-specific peaks back over to the mouse genome
-system("liftOver -bedPlus=4 promoters/clustered/E10.5_promoter_mouse.specific_smiCra_50bpsummits.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E10.5_promoter_mouse.specific_smiCra_50bpsummits_backTOmm10.bed promoters/clustered/E10.5_promoter_mouse.specific_smiCra_50bpsummits_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E11.5_promoter_mouse.specific_smiCra_50bpsummits.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E11.5_promoter_mouse.specific_smiCra_50bpsummits_backTOmm10.bed promoters/clustered/E11.5_promoter_mouse.specific_smiCra_50bpsummits_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E12.5_promoter_mouse.specific_smiCra_50bpsummits.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E12.5_promoter_mouse.specific_smiCra_50bpsummits_backTOmm10.bed promoters/clustered/E12.5_promoter_mouse.specific_smiCra_50bpsummits_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E13.5_promoter_mouse.specific_smiCra_50bpsummits.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E13.5_promoter_mouse.specific_smiCra_50bpsummits_backTOmm10.bed promoters/clustered/E13.5_promoter_mouse.specific_smiCra_50bpsummits_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E14.5_promoter_mouse.specific_smiCra_50bpsummits.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E14.5_promoter_mouse.specific_smiCra_50bpsummits_backTOmm10.bed promoters/clustered/E14.5_promoter_mouse.specific_smiCra_50bpsummits_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E15.5_promoter_mouse.specific_smiCra_50bpsummits.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E15.5_promoter_mouse.specific_smiCra_50bpsummits_backTOmm10.bed promoters/clustered/E15.5_promoter_mouse.specific_smiCra_50bpsummits_backTOmm10_unmapped.bed",intern=TRUE)
-
-system("liftOver -bedPlus=4 enhancers/E10.5_enhancer_mouse.specific_smiCra_50bpsummits.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E10.5_enhancer_mouse.specific_smiCra_50bpsummits_backTOmm10.bed enhancers/E10.5_enhancer_mouse.specific_smiCra_50bpsummits_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E11.5_enhancer_mouse.specific_smiCra_50bpsummits.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E11.5_enhancer_mouse.specific_smiCra_50bpsummits_backTOmm10.bed enhancers/E11.5_enhancer_mouse.specific_smiCra_50bpsummits_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E12.5_enhancer_mouse.specific_smiCra_50bpsummits.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E12.5_enhancer_mouse.specific_smiCra_50bpsummits_backTOmm10.bed enhancers/E12.5_enhancer_mouse.specific_smiCra_50bpsummits_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E13.5_enhancer_mouse.specific_smiCra_50bpsummits.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E13.5_enhancer_mouse.specific_smiCra_50bpsummits_backTOmm10.bed enhancers/E13.5_enhancer_mouse.specific_smiCra_50bpsummits_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E14.5_enhancer_mouse.specific_smiCra_50bpsummits.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E14.5_enhancer_mouse.specific_smiCra_50bpsummits_backTOmm10.bed enhancers/E14.5_enhancer_mouse.specific_smiCra_50bpsummits_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E15.5_enhancer_mouse.specific_smiCra_50bpsummits.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E15.5_enhancer_mouse.specific_smiCra_50bpsummits_backTOmm10.bed enhancers/E15.5_enhancer_mouse.specific_smiCra_50bpsummits_backTOmm10_unmapped.bed",intern=TRUE)
-
-## Lift dunnart-specific peaks and combined peaks back into mm10 coordinates for GREAT analysis
-system("liftOver -bedPlus=4 promoters/clustered/E10.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E10.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10.bed promoters/clustered/E10.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E11.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E11.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10.bed promoters/clustered/E11.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E12.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E12.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10.bed promoters/clustered/E12.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E13.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E13.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10.bed promoters/clustered/E13.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E14.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E14.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10.bed promoters/clustered/E14.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E15.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E15.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10.bed promoters/clustered/E15.5.clustered_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-
-system("liftOver -bedPlus=4 enhancers/E10.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E10.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10.bed enhancers/E10.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E11.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E11.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10.bed enhancers/E11.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E12.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E12.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10.bed enhancers/E12.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E13.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E13.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10.bed enhancers/E13.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E14.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E14.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10.bed enhancers/E14.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E15.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E15.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10.bed enhancers/E15.5_enhancer_dunnart.specific_mm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-
-## Combined peaks
-
-system("liftOver -bedPlus=4 promoters/clustered/E10.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E10.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10.bed promoters/clustered/E10.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E11.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E11.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10.bed promoters/clustered/E11.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E12.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E12.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10.bed promoters/clustered/E12.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E13.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E13.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10.bed promoters/clustered/E13.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E14.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E14.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10.bed promoters/clustered/E14.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 promoters/clustered/E15.5_promoterOverlapmm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain promoters/clustered/E15.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10.bed promoters/clustered/E15.5_promoterOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-
-system("liftOver -bedPlus=4 enhancers/E10.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E10.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10.bed enhancers/E10.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E11.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E11.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10.bed enhancers/E11.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E12.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E12.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10.bed enhancers/E12.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E13.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E13.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10.bed enhancers/E13.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E14.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E14.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10.bed enhancers/E14.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-system("liftOver -bedPlus=4 enhancers/E15.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed ../smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain enhancers/E15.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10.bed enhancers/E15.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra_backTOmm10_unmapped.bed",intern=TRUE)
-
-
-###################################################################################################
-################################### INTERSECT IDS FROM OVERLAPS ###################################
-###################################################################################################
-
-
-
-
-
-###################################################################################################
-############################### GENE ONTOLOGY & PATHWAY ANALYSIS ##################################
-###################################################################################################
-## Using mouse coordinates for the peaks, use GREAT to look for the nearest gene TSS
-## Then use clusterProfiler to look at Gene Ontology enrichment in the mouse, dunnart and combined peak sets
-
-library(rGREAT)
-library(clusterProfiler)
-library(data.table)
-
-
-great <- function(bedList){
- bedFiles = list.files(bedList, pattern= ".bed", full.names=T) # create list of files in directory
- bedFiles = as.list(bedFiles)
- data = lapply(bedFiles, function(x) fread(x, header=TRUE, sep="\t", quote = "") %>% as.data.table()) # read in all files
- data = lapply(data, function(x) submitGreatJob(x, species = "mm10")) # submit GREAT jobs
- names(data) = c("E10:mouse", "E10:combined", "E10:dunnart", "E11:mouse", "E11:combined", "E11:dunnart",
- "E12:mouse", "E12:combined", "E12:dunnart", "E13:mouse", "E13:combined", "E13:dunnart",
- "E14:mouse", "E14:combined", "E14:dunnart", "E15:mouse", "E15:combined", "E15:dunnart")
-
- data = Map(mutate, data, group = names(data)) ## add column with group names
-
- databind = rbindlist(data,) #bind dataframes together
- split_by_stage = databind[
- ,c("stage", "species") := tstrsplit(group, ":", fixed=TRUE)
- ][
- ,'group':=NULL
- ]
-
-
-}
-
-
-
-
-## For each mouse stage have a list of peak IDs
-
-# ## Scan IDs into an object
-# setwd("/data/projects/punim0586/lecook/chipseq-pipeline/cross_species/peakAnnotation/consensus/enhancers")
-# E10 <- scan("E10.5_enhancerOverlapmm10_50bpsummitsIDs.txt", what="", sep="\n")
-# E11 <- scan("E11.5_enhancerOverlapmm10_50bpsummitsIDs.txt", what="", sep="\n")
-# E12 <- scan("E12.5_enhancerOverlapmm10_50bpsummitsIDs.txt", what="", sep="\n")
-# E13 <- scan("E13.5_enhancerOverlapmm10_50bpsummitsIDs.txt", what="", sep="\n")
-# E14 <- scan("E14.5_enhancerOverlapmm10_50bpsummitsIDs.txt", what="", sep="\n")
-# E15 <- scan("E15.5_enhancerOverlapmm10_50bpsummitsIDs.txt", what="", sep="\n")
-
-# ## Look for dunnart peak IDs that overlap with mouse embryonic stages in the mouse peaks that overlap with the dunnart peaks at P0
-# # E10.5_enhancerOverlapsmiCra_50bpsummits.bed file:
-# # chr8 121436317 121436374 H3K27ac_pooled_macs2_peak_644 9.64793 chr8 121436230 121436873 E10.5_H3K27ac.pooled.macs2_peak_77013 75 . 4.66414 7.52876 5.17964 305 57
-
-# write.table(subset(read.table("E10.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), unique(E10) %in% V4), file = "E10.5_enhancerOverlapmm10_smiCra1_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E11.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), unique(E11) %in% V4), file = "E11.5_enhancerOverlapmm10_smiCra1_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E12.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), unique(E12) %in% V4), file = "E12.5_enhancerOverlapmm10_smiCra1_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E13.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), unique(E13) %in% V4), file = "E13.5_enhancerOverlapmm10_smiCra1_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E14.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), unique(E14) %in% V4), file = "E14.5_enhancerOverlapmm10_smiCra1_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E15.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), unique(E15) %in% V4), file = "E15.5_enhancerOverlapmm10_smiCra1_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-
-# ## Mouse CREs with dunnart coordinates that aren't active in dunnart at P0
-# ## Do I use only those that are reproducible (eg. found in both lists)or even those that I overlapped from mouse to dunnart but not in the finally overlap??
-
-# write.table(subset(read.table("E10.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), !(E10 %in% V4)), file = "E10.5_enhancerNoOverlapmm10_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E11.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), !(E10 %in% V4)), file = "E11.5_enhancerNoOverlapmm10_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E12.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), !(E10 %in% V4), file = "E12.5_enhancerNoOverlapmm10_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E13.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), !(E10 %in% V4)), file = "E13.5_enhancerNoOverlapmm10_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E14.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), !(E10 %in% V4)), file = "E14.5_enhancerNoOverlapmm10_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E15.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), !(E10 %in% V4)), file = "E15.5_enhancerNoOverlapmm10_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-
-# ## Not in list dunnart CREs
-# write.table(subset(read.table("E10.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), !(E10 %in% V4)), file = "E10.5_enhancerNoOverlasmiCra1_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E11.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), !(V4 %in% E11)), file = "E11.5_enhancerNoOverlapmm10_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E12.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), !(V4 %in% E12), file = "E12.5_enhancerNoOverlapmm10_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E13.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), !(V4 %in% E13)), file = "E13.5_enhancerNoOverlapmm10_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E14.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), !(V4 %in% E14)), file = "E14.5_enhancerNoOverlapmm10_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E15.5_enhancerOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), !(V4 %in% E15)), file = "E15.5_enhancerNoOverlapmm10_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-
-# ## Promoters
-# setwd("/data/projects/punim0586/lecook/chipseq-pipeline/cross_species/peakAnnotation/overlaps/promoters/clustered/")
-# E10 <- scan("E10.5_promoterOverlapmm10_50bpsummitsIDs.txt", what="", sep="\n")
-# E11 <- scan("E11.5_promoterOverlapmm10_50bpsummitsIDs.txt", what="", sep="\n")
-# E12 <- scan("E12.5_promoterOverlapmm10_50bpsummitsIDs.txt", what="", sep="\n")
-# E13 <- scan("E13.5_promoterOverlapmm10_50bpsummitsIDs.txt", what="", sep="\n")
-# E14 <- scan("E14.5_promoterOverlapmm10_50bpsummitsIDs.txt", what="", sep="\n")
-# E15 <- scan("E15.5_promoterOverlapmm10_50bpsummitsIDs.txt", what="", sep="\n")
-
-# ## Look for dunnart peak IDs that overlap with mouse embryonic stages in the mouse peaks that overlap with the dunnart peaks at P0
-# write.table(subset(read.table("E10.5_promoterOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), unique(E10) %in% V4), file = "E10.5_promoterOverlapmm10_smiCra1_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E11.5_promoterOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), unique(E11) %in% V4), file = "E11.5_promoterOverlapmm10_smiCra1_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E12.5_promoterOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), unique(E12) %in% V4), file = "E12.5_promoterOverlapmm10_smiCra1_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E13.5_promoterOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), unique(E13) %in% V4), file = "E13.5_promoterOverlapmm10_smiCra1_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E14.5_promoterOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), unique(E14) %in% V4), file = "E14.5_promoterOverlapmm10_smiCra1_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-# write.table(subset(read.table("E15.5_promoterOverlapsmiCra_50bpsummits.bed", sep="\t", quote="", header=FALSE), unique(E15) %in% V4), file = "E15.5_promoterOverlapmm10_smiCra1_50bpsummits.bed", quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
-
-# ## Check duplicates
-# awk 'x[$4]++ == 1 { print $4 " is duplicated"}' E10.5_enhancerOverlapmm10_50bpsummits.bed
-# awk 'x[$4]++ == 1 { print $4 " is duplicated"}' E11.5_enhancerOverlapmm10_50bpsummits.bed
-# awk 'x[$4]++ == 1 { print $4 " is duplicated"}' E12.5_enhancerOverlapmm10_50bpsummits.bed
-# awk 'x[$4]++ == 1 { print $4 " is duplicated"}' E13.5_enhancerOverlapmm10_50bpsummits.bed
-# awk 'x[$4]++ == 1 { print $4 " is duplicated"}' E15.5_enhancerOverlapmm10_50bpsummits.bed
-# awk 'x[$4]++ == 1 { print $4 " is duplicated"}' E14.5_enhancerOverlapmm10_50bpsummits.bed
-
-
-
-
-# awk 'x[$9]++ == 1 { print $9 " is duplicated"}' E10.5_enhancerOverlapmm10_50bpsummits_backTOsmiCra.bed
\ No newline at end of file