Update Enhancer processing.

intervene_test/GRO-seq_enhancers.bed

@@ -61,7 +61,6 @@ chr1	26852899	26853099
 chr1	28859349	28861399
 chr1	31967299	31970599
 chr1	31967299	31970649
-chr1	31967299	31970649
 chr1	34943399	34944299
 chr1	34943399	34944299
 chr1	37202049	37202149
@@ -187,7 +186,6 @@ chr1	121476249	121485499
 chr1	121477749	121485499
 chr1	143278349	143284949
 chr1	143645749	143650049
-chr1	143645749	143650049
 chr1	143646449	143647699
 chr1	143646449	143647799
 chr1	143879649	143879999
@@ -582,15 +580,12 @@ chr11	12741449	12741649
 chr11	14135049	14135699
 chr11	15551249	15551699
 chr11	15551249	15551699
-chr11	15551249	15551699
 chr11	16775399	16776199
 chr11	16776099	16776249
 chr11	16863749	16864249
 chr11	21022299	21022599
 chr11	21613949	21616899
 chr11	21613949	21616899
-chr11	21613949	21616899
-chr11	22173049	22175699
 chr11	22173049	22175699
 chr11	22173049	22175699
 chr11	22173999	22175049
@@ -601,7 +596,6 @@ chr11	22174899	22175049
 chr11	22904449	22905449
 chr11	22904449	22905449
 chr11	22904449	22905899
-chr11	22904449	22905899
 chr11	23343199	23348699
 chr11	23343199	23348699
 chr11	25564699	25564899
@@ -611,8 +605,6 @@ chr11	29761149	29761399
 chr11	32395349	32395499
 chr11	32395349	32396449
 chr11	32395349	32396449
-chr11	32395349	32396449
-chr11	33271799	33273699
 chr11	33271799	33273699
 chr11	33272799	33273399
 chr11	40607549	40607699
@@ -621,12 +613,10 @@ chr11	43670299	43670399
 chr11	45847199	45848349
 chr11	45847199	45848399
 chr11	45847199	45848499
-chr11	45847199	45848499
 chr11	45847299	45848399
 chr11	45848049	45848499
 chr11	46094649	46094949
 chr11	55744399	55746349
-chr11	55744399	55746599
 chr11	55745699	55746599
 chr11	57805149	57805299
 chr11	57805149	57805499
@@ -1989,7 +1979,6 @@ chr2	117017699	117019399
 chr2	117017699	117019399
 chr2	117765699	117770399
 chr2	117765699	117770399
-chr2	117765699	117770399
 chr2	118038949	118039549
 chr2	118039299	118040249
 chr2	118039349	118039599
@@ -2990,7 +2979,6 @@ chr3	190142249	190143049
 chr3	191358949	191359249
 chr3	191612699	191618749
 chr3	191613199	191618899
-chr3	191613199	191618899
 chr3	191616799	191617549
 chr3	191643999	191648249
 chr3	191643999	191648249
@@ -4720,21 +4708,17 @@ chrX	46230749	46231249
 chrX	46492749	46492899
 chrX	46492749	46493399
 chrX	46966299	46970199
-chrX	46966299	46970199
 chrX	46966599	46970199
 chrX	48012699	48013549
 chrX	49935249	49936499
-chrX	49935249	49936499
 chrX	49935799	49936499
 chrX	49935799	49936499
 chrX	49935799	49936499
 chrX	51207299	51211549
-chrX	51207299	51211549
 chrX	51209399	51209949
 chrX	53797449	53799799
 chrX	53797449	53799799
 chrX	54082549	54089649
-chrX	54082549	54089649
 chrX	54087599	54088949
 chrX	56956749	56958299
 chrX	56956749	56958299
@@ -4809,7 +4793,6 @@ chrX	103015199	103015399
 chrX	103021399	103022699
 chrX	106740199	106745549
 chrX	108296049	108302549
-chrX	108296049	108302549
 chrX	108297299	108301199
 chrX	108297299	108301199
 chrX	108297299	108301199
@@ -4937,14 +4920,12 @@ chrY	4212349	4212999
 chrY	4212799	4212949
 chrY	4391849	4393749
 chrY	4391849	4393749
-chrY	4391849	4393749
 chrY	4392249	4392849
 chrY	5190449	5190599
 chrY	5193949	5194099
 chrY	5505949	5506249
 chrY	5844699	5850099
 chrY	5844699	5850099
-chrY	5844699	5850099
 chrY	5844899	5846299
 chrY	5844899	5846299
 chrY	5844899	5846299

intervene_test/Intervene_results/Intervene_Shiny_App_genomic_UpSet_module_import.txt

 You can go to Intervene Shiny App https://asntech.shinyapps.io/Intervene-app/ and copy/paste the following intersection data to get more interactive figures.
 
-H3K27ac_enhancers=12510,H3K27ac_enhancers&H3K4me1_enhancers=55566,H3K4me1_enhancers=153327,GRO-seq_enhancers&H3K27ac_enhancers&H3K4me1_enhancers=610,GRO-seq_enhancers&H3K27ac_enhancers=257,GRO-seq_enhancers=3781,GRO-seq_enhancers&H3K4me1_enhancers=360
+H3K27ac_enhancers=12510,H3K27ac_enhancers&H3K4me1_enhancers=55566,H3K4me1_enhancers=153327,GRO-seq_enhancers&H3K27ac_enhancers&H3K4me1_enhancers=610,GRO-seq_enhancers&H3K27ac_enhancers=256,GRO-seq_enhancers=3765,GRO-seq_enhancers&H3K4me1_enhancers=358
\ No newline at end of file

intervene_test/Intervene_results/intervene_genomic_UpSet_plot.R

@@ -2,6 +2,6 @@
 if (suppressMessages(!require("UpSetR"))) suppressMessages(install.packages("UpSetR", repos="http://cran.us.r-project.org"))
 library("UpSetR")
 pdf("/Users/venkatmalladi/Projects/PITTED/intervene_test/Intervene_results/intervene_genomic_UpSet_plot.pdf", width=10, height=8, onefile=FALSE)
-expressionInput <- c('H3K27ac_enhancers'=12510,'H3K27ac_enhancers&H3K4me1_enhancers'=55566,'H3K4me1_enhancers'=153327,'GRO-seq_enhancers&H3K27ac_enhancers&H3K4me1_enhancers'=610,'GRO-seq_enhancers&H3K27ac_enhancers'=257,'GRO-seq_enhancers'=3781,'GRO-seq_enhancers&H3K4me1_enhancers'=360)
+expressionInput <- c('H3K27ac_enhancers'=12510,'H3K27ac_enhancers&H3K4me1_enhancers'=55566,'H3K4me1_enhancers'=153327,'GRO-seq_enhancers&H3K27ac_enhancers&H3K4me1_enhancers'=610,'GRO-seq_enhancers&H3K27ac_enhancers'=256,'GRO-seq_enhancers'=3765,'GRO-seq_enhancers&H3K4me1_enhancers'=358)
 upset(fromExpression(expressionInput), nsets=3, nintersects=30, show.numbers="yes", main.bar.color="#108DCC", sets.bar.color="#E62128", empty.intersections=NULL, order.by = "degree", number.angles = 0, mainbar.y.label ="No. of Intersections", sets.x.label ="No. of Unique Enhancers")
 invisible(dev.off())

intervene_test/intervene_figure.sh

@@ -4,7 +4,7 @@
 cp ../H3K4me1_filtered_peaks.bed H3K4me1_enhancers.bed
 cp ../H3K27ac_filtered_peaks.bed H3K27ac_enhancers.bed
 cp  ../SUNP_filtered_peaks.bed .
-cp  ../SUNP_filtered_peaks.bed .
+cp  ../SSP_filtered_peaks_merged.bed .
 cut -f1,2,3  SUNP_filtered_peaks.bed > t
 cut -f1,2,3 SSP_filtered_peaks_merged.bed >> t
 sort-bed t > GRO-seq_enhancers.bed