From c8f21f9616203a8ca5cac5cd9fd4857317fb5dff Mon Sep 17 00:00:00 2001
From: Venkat Malladi <Venkat.Malladi@utsouthwestern.edu>
Date: Tue, 21 Feb 2017 13:42:56 -0600
Subject: [PATCH] Overlap of enhancers plot.
---
intervene_test/GRO-seq_enhancers.bed | 1324 +
intervene_test/GRO-seq_filtered_peaks.bed | 2018 +
intervene_test/H3K27ac_enhancers.bed | 68516 +++++
intervene_test/H3K4me1_enhancers.bed | 208260 +++++++++++++++
..._Shiny_App_genomic_UpSet_module_import.txt | 3 +
.../intervene_genomic_UpSet_plot.R | 7 +
.../intervene_genomic_UpSet_plot.pdf | Bin 0 -> 6268 bytes
intervene_test/SSP_filtered_peaks_merged.bed | 1314 +
intervene_test/SUNP_filtered_peaks.bed | 704 +
intervene_test/intervene_figure.sh | 12 +
10 files changed, 282158 insertions(+)
create mode 100644 intervene_test/GRO-seq_enhancers.bed
create mode 100644 intervene_test/GRO-seq_filtered_peaks.bed
create mode 100644 intervene_test/H3K27ac_enhancers.bed
create mode 100644 intervene_test/H3K4me1_enhancers.bed
create mode 100644 intervene_test/Intervene_results/Intervene_Shiny_App_genomic_UpSet_module_import.txt
create mode 100755 intervene_test/Intervene_results/intervene_genomic_UpSet_plot.R
create mode 100644 intervene_test/Intervene_results/intervene_genomic_UpSet_plot.pdf
create mode 100644 intervene_test/SSP_filtered_peaks_merged.bed
create mode 100644 intervene_test/SUNP_filtered_peaks.bed
create mode 100644 intervene_test/intervene_figure.sh
diff --git a/intervene_test/GRO-seq_enhancers.bed b/intervene_test/GRO-seq_enhancers.bed
new file mode 100644
index 0000000..d17b298
--- /dev/null
+++ b/intervene_test/GRO-seq_enhancers.bed
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diff --git a/intervene_test/GRO-seq_filtered_peaks.bed b/intervene_test/GRO-seq_filtered_peaks.bed
new file mode 100644
index 0000000..b53f8ed
--- /dev/null
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diff --git a/intervene_test/H3K27ac_enhancers.bed b/intervene_test/H3K27ac_enhancers.bed
new file mode 100644
index 0000000..de85ef7
--- /dev/null
+++ b/intervene_test/H3K27ac_enhancers.bed
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diff --git a/intervene_test/H3K4me1_enhancers.bed b/intervene_test/H3K4me1_enhancers.bed
new file mode 100644
index 0000000..4b47025
--- /dev/null
+++ b/intervene_test/H3K4me1_enhancers.bed
@@ -0,0 +1,208260 @@
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diff --git a/intervene_test/Intervene_results/Intervene_Shiny_App_genomic_UpSet_module_import.txt b/intervene_test/Intervene_results/Intervene_Shiny_App_genomic_UpSet_module_import.txt
new file mode 100644
index 0000000..c1a9edd
--- /dev/null
+++ b/intervene_test/Intervene_results/Intervene_Shiny_App_genomic_UpSet_module_import.txt
@@ -0,0 +1,3 @@
+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=12592,H3K27ac_enhancers&H3K4me1_enhancers=55720,H3K4me1_enhancers=153356,GRO-seq_enhancers&H3K27ac_enhancers&H3K4me1_enhancers=179,GRO-seq_enhancers&H3K27ac_enhancers=49,GRO-seq_enhancers=907,GRO-seq_enhancers&H3K4me1_enhancers=189
\ No newline at end of file
diff --git a/intervene_test/Intervene_results/intervene_genomic_UpSet_plot.R b/intervene_test/Intervene_results/intervene_genomic_UpSet_plot.R
new file mode 100755
index 0000000..ff3739a
--- /dev/null
+++ b/intervene_test/Intervene_results/intervene_genomic_UpSet_plot.R
@@ -0,0 +1,7 @@
+#!/usr/bin/env Rscript
+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'=12592,'H3K27ac_enhancers&H3K4me1_enhancers'=55720,'H3K4me1_enhancers'=153356,'GRO-seq_enhancers&H3K27ac_enhancers&H3K4me1_enhancers'=179,'GRO-seq_enhancers&H3K27ac_enhancers'=49,'GRO-seq_enhancers'=907,'GRO-seq_enhancers&H3K4me1_enhancers'=189)
+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())
diff --git a/intervene_test/Intervene_results/intervene_genomic_UpSet_plot.pdf b/intervene_test/Intervene_results/intervene_genomic_UpSet_plot.pdf
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diff --git a/intervene_test/SSP_filtered_peaks_merged.bed b/intervene_test/SSP_filtered_peaks_merged.bed
new file mode 100644
index 0000000..2369f3e
--- /dev/null
+++ b/intervene_test/SSP_filtered_peaks_merged.bed
@@ -0,0 +1,1314 @@
+chr2 14536049 14542999 SSP_100925
+chr1 160595699 160600699 SSP_10167
+chr1 160621649 160622949 SSP_10168
+chr1 160622099 160625999 SSP_10169
+chr2 35002849 35004999 SSP_102194
+chr2 35003099 35007399 SSP_102195
+chr2 35661999 35667699 SSP_102280
+chr2 49599749 49602749 SSP_103347
+chr1 163580299 163585449 SSP_10344
+chr2 64479549 64487649 SSP_104436
+chr2 64479549 64487649 SSP_104437
+chr2 65097299 65103249 SSP_104492
+chr2 65097299 65104949 SSP_104493
+chr2 67555599 67561899 SSP_104597
+chr2 67558899 67565899 SSP_104598
+chr2 67558899 67565899 SSP_104599
+chr2 68008949 68009149 SSP_104677
+chr2 76665349 76672599 SSP_105290
+chr2 76665349 76672599 SSP_105291
+chr2 76665349 76672599 SSP_105292
+chr2 78922999 78931199 SSP_105515
+chr2 81617949 81626799 SSP_105788
+chr2 82195199 82197899 SSP_105859
+chr2 83765049 83767499 SSP_106320
+chr2 84503449 84503649 SSP_106517
+chr2 84503499 84503649 SSP_106518
+chr2 104751099 104762599 SSP_107760
+chr2 106882049 106882199 SSP_108094
+chr2 107700949 107704399 SSP_108208
+chr2 107703349 107705749 SSP_108209
+chr2 107701699 107710199 SSP_108210
+chr2 108220499 108224549 SSP_108307
+chr2 108220499 108224549 SSP_108308
+chr2 122596699 122598599 SSP_109607
+chr2 124112549 124116499 SSP_110006
+chr2 124536249 124543599 SSP_110139
+chr2 126881649 126881799 SSP_110535
+chr2 132374599 132389999 SSP_111281
+chr2 132381149 132389999 SSP_111282
+chr2 132381149 132389999 SSP_111283
+chr2 132381149 132390249 SSP_111284
+chr2 132381149 132389999 SSP_111285
+chr2 132381149 132390649 SSP_111286
+chr2 137063599 137063949 SSP_111647
+chr2 143008849 143013199 SSP_112367
+chr2 143008849 143015849 SSP_112368
+chr2 143008849 143013499 SSP_112369
+chr2 143627799 143629999 SSP_112543
+chr2 143627799 143631299 SSP_112544
+chr2 151716099 151717599 SSP_113693
+chr2 153660599 153664999 SSP_113795
+chr2 153660599 153667749 SSP_113796
+chr2 153664649 153673149 SSP_113797
+chr2 153664849 153673149 SSP_113798
+chr2 153664849 153673149 SSP_113799
+chr2 153664849 153673149 SSP_113800
+chr2 161734299 161740649 SSP_114523
+chr2 161735949 161740649 SSP_114524
+chr2 161735999 161741649 SSP_114525
+chr2 161737849 161741649 SSP_114526
+chr2 161737849 161741649 SSP_114527
+chr2 162128449 162140449 SSP_114584
+chr2 162995249 162999649 SSP_114610
+chr2 162995249 162999649 SSP_114611
+chr2 162995249 162999649 SSP_114614
+chr2 162995249 162999649 SSP_114616
+chr1 180488099 180488299 SSP_11469
+chr2 167393799 167396049 SSP_114923
+chr2 167393849 167396049 SSP_114925
+chr2 169776599 169778499 SSP_115066
+chr2 172464999 172471849 SSP_115129
+chr2 172470849 172475849 SSP_115130
+chr2 188522499 188525799 SSP_116374
+chr2 188531999 188540599 SSP_116377
+chr2 190080999 190086549 SSP_116425
+chr2 194211949 194217649 SSP_116920
+chr2 194211999 194219399 SSP_116921
+chr2 194211999 194217699 SSP_116922
+chr2 194212099 194217699 SSP_116923
+chr2 194212199 194217699 SSP_116924
+chr2 210161799 210169549 SSP_118171
+chr2 224086249 224086849 SSP_119115
+chr2 224086249 224086899 SSP_119116
+chr1 187330999 187337149 SSP_11951
+chr1 187330999 187337149 SSP_11952
+chr1 187331749 187340299 SSP_11953
+chr1 187330999 187337149 SSP_11954
+chr1 187335099 187340299 SSP_11955
+chr1 187330999 187337149 SSP_11956
+chr1 187335099 187340899 SSP_11957
+chr1 187335099 187340299 SSP_11958
+chr1 187335099 187340449 SSP_11959
+chr2 227339499 227344349 SSP_119657
+chr2 227340849 227350199 SSP_119658
+chr2 227367749 227372749 SSP_119672
+chr2 227367749 227372749 SSP_119673
+chr2 227367749 227372749 SSP_119674
+chr2 227367749 227372749 SSP_119675
+chr2 227371599 227372749 SSP_119677
+chr2 227372599 227373149 SSP_119678
+chr2 228261349 228267299 SSP_119768
+chr2 231833299 231835949 SSP_119969
+chr2 231833299 231840499 SSP_119970
+chr2 231833299 231840499 SSP_119971
+chr2 235466499 235475599 SSP_120180
+chr2 235470249 235475599 SSP_120182
+chr2 235470849 235475599 SSP_120184
+chr2 237486399 237495399 SSP_120422
+chr2 237486399 237495399 SSP_120423
+chr2 237486399 237495449 SSP_120424
+chr2 237773099 237777099 SSP_120483
+chr2 237773099 237777099 SSP_120484
+chr2 237773099 237778049 SSP_120485
+chr20 4059849 4066499 SSP_121160
+chr20 4550999 4557299 SSP_121235
+chr20 5870649 5875949 SSP_121322
+chr20 6726899 6731699 SSP_121467
+chr20 6726899 6731699 SSP_121468
+chr20 17159599 17168849 SSP_122371
+chr20 18240399 18246499 SSP_122437
+chr20 18240399 18250149 SSP_122439
+chr20 18241999 18250149 SSP_122440
+chr20 18246349 18249099 SSP_122441
+chr20 21093299 21095899 SSP_122656
+chr20 21735349 21736349 SSP_122689
+chr20 21735399 21736349 SSP_122690
+chr20 21735399 21737549 SSP_122691
+chr20 21735349 21737399 SSP_122692
+chr20 21735849 21737399 SSP_122693
+chr20 21735849 21737549 SSP_122694
+chr20 22618749 22619149 SSP_122889
+chr20 22664249 22667499 SSP_122900
+chr20 23849049 23851599 SSP_123161
+chr20 23849049 23854349 SSP_123162
+chr20 30039699 30044399 SSP_123552
+chr20 31559149 31564649 SSP_123570
+chr20 31561149 31569899 SSP_123571
+chr20 31561149 31569899 SSP_123572
+chr20 40418799 40422749 SSP_124169
+chr20 46921999 46924399 SSP_124572
+chr20 52771449 52778899 SSP_124893
+chr20 57193699 57195599 SSP_125741
+chr20 59175849 59176299 SSP_125922
+chr20 59496249 59499999 SSP_126047
+chr20 59585299 59589749 SSP_126064
+chr20 59585299 59592599 SSP_126066
+chr20 59585299 59589749 SSP_126067
+chr21 9696349 9700699 SSP_126256
+chr21 10492199 10500399 SSP_126341
+chr21 10632699 10644749 SSP_126361
+chr21 18825799 18829499 SSP_127097
+chr21 20230049 20230899 SSP_127189
+chr21 20230049 20230899 SSP_127190
+chr21 25733299 25739549 SSP_128482
+chr21 25735949 25739549 SSP_128483
+chr21 25735949 25743849 SSP_128484
+chr21 25733299 25739549 SSP_128485
+chr21 25739149 25739549 SSP_128486
+chr21 25739149 25743849 SSP_128487
+chr21 25739199 25739549 SSP_128488
+chr21 25739199 25743849 SSP_128489
+chr21 26526099 26527699 SSP_128661
+chr21 28253599 28262249 SSP_128786
+chr21 28254999 28258549 SSP_128791
+chr22 20193549 20194199 SSP_130238
+chr22 28122499 28126649 SSP_130636
+chr22 28122499 28126649 SSP_130637
+chr22 32432449 32435999 SSP_130682
+chr22 49430099 49430499 SSP_131637
+chr1 193391249 193396749 SSP_13201
+chr1 193552499 193559499 SSP_13237
+chr3 13839599 13839749 SSP_132627
+chr3 13839449 13848399 SSP_132628
+chr3 16591899 16592849 SSP_132728
+chr1 193830849 193832799 SSP_13299
+chr3 21003299 21005499 SSP_133029
+chr3 21007349 21014499 SSP_133030
+chr3 22737749 22739299 SSP_133209
+chr3 22737749 22739299 SSP_133210
+chr3 29087949 29088099 SSP_133881
+chr3 29087949 29088899 SSP_133882
+chr3 31046299 31046449 SSP_134116
+chr3 33143849 33144899 SSP_134333
+chr1 194531849 194536349 SSP_13504
+chr3 45199999 45203449 SSP_135299
+chr3 56510349 56517899 SSP_135655
+chr3 56516249 56516549 SSP_135656
+chr3 74886249 74890699 SSP_137089
+chr3 74887249 74894199 SSP_137090
+chr3 75263499 75272299 SSP_137216
+chr3 83600299 83605299 SSP_138290
+chr3 84279549 84287099 SSP_138488
+chr3 84279549 84287099 SSP_138489
+chr3 84279549 84288599 SSP_138490
+chr1 195784799 195792299 SSP_13868
+chr3 86601399 86602449 SSP_138696
+chr1 195877799 195878199 SSP_13873
+chr1 195877849 195878199 SSP_13874
+chr3 87646299 87654099 SSP_138992
+chr3 87651799 87654049 SSP_138993
+chr3 88939749 88944399 SSP_139267
+chr3 90141849 90148199 SSP_139465
+chr3 90146049 90148199 SSP_139466
+chr3 90146249 90148199 SSP_139467
+chr3 90188549 90189849 SSP_139472
+chr3 95404799 95406049 SSP_139936
+chr3 95404799 95406049 SSP_139937
+chr3 98998299 99003949 SSP_140407
+chr3 99001049 99003949 SSP_140410
+chr3 103467149 103473199 SSP_140874
+chr3 103877699 103880649 SSP_140986
+chr3 108882649 108890899 SSP_141577
+chr3 108882649 108890899 SSP_141578
+chr3 108887449 108890899 SSP_141579
+chr1 198750799 198759749 SSP_14188
+chr3 135637449 135644899 SSP_142868
+chr3 141537099 141546249 SSP_143307
+chr3 141537099 141544199 SSP_143308
+chr3 147088499 147088699 SSP_143965
+chr3 149955349 149960599 SSP_144266
+chr3 149955349 149960599 SSP_144267
+chr3 161680349 161687199 SSP_145241
+chr3 161680349 161687199 SSP_145242
+chr3 161680349 161687199 SSP_145243
+chr3 161680349 161687199 SSP_145244
+chr3 161683299 161687199 SSP_145245
+chr3 161684199 161689899 SSP_145246
+chr3 169912849 169921349 SSP_146426
+chr3 175996299 176003549 SSP_146659
+chr3 176017199 176020599 SSP_146661
+chr3 176029349 176032949 SSP_146662
+chr3 176047899 176053549 SSP_146663
+chr3 179871949 179881349 SSP_146917
+chr3 179871949 179880249 SSP_146918
+chr1 24585949 24590349 SSP_1470
+chr3 187707599 187708899 SSP_147486
+chr3 189860299 189873899 SSP_147622
+chr3 189864699 189873899 SSP_147623
+chr3 189867799 189873899 SSP_147624
+chr3 189860299 189868049 SSP_147625
+chr3 189887699 189892649 SSP_147632
+chr3 189888749 189896399 SSP_147633
+chr3 189888699 189896399 SSP_147634
+chr1 208603149 208607799 SSP_14776
+chr3 191356899 191359249 SSP_147834
+chr3 191612399 191618449 SSP_147896
+chr3 191613099 191617549 SSP_147897
+chr3 191615349 191618449 SSP_147898
+chr3 191646349 191646749 SSP_147907
+chr3 194633499 194640149 SSP_148158
+chr3 194633499 194640049 SSP_148159
+chr4 8350999 8362270 SSP_148491
+chr4 8353699 8362270 SSP_148492
+chr4 8353699 8362270 SSP_148493
+chr4 9395549 9399049 SSP_148604
+chr4 17396749 17398999 SSP_149310
+chr4 18574549 18576899 SSP_149508
+chr4 18574549 18578049 SSP_149510
+chr4 18574649 18578049 SSP_149511
+chr4 24314749 24322899 SSP_150076
+chr4 24319149 24321049 SSP_150077
+chr4 27645249 27645549 SSP_150473
+chr4 27645249 27645649 SSP_150475
+chr4 27731199 27732249 SSP_150502
+chr1 25478149 25483699 SSP_1511
+chr1 25478149 25483699 SSP_1512
+chr1 25482299 25485199 SSP_1513
+chr1 25482299 25485199 SSP_1514
+chr1 211344599 211348499 SSP_15141
+chr1 211344599 211348499 SSP_15141
+chr1 25482299 25489099 SSP_1515
+chr4 32665549 32668299 SSP_151667
+chr4 36907399 36915049 SSP_152617
+chr1 214246499 214253299 SSP_15289
+chr4 42259249 42261599 SSP_152980
+chr1 214335749 214340549 SSP_15326
+chr4 45220149 45223399 SSP_153546
+chr4 49326599 49332399 SSP_153903
+chr4 49326599 49338649 SSP_153904
+chr4 49507649 49518549 SSP_153910
+chr4 55890949 55895349 SSP_154214
+chr4 55890949 55895349 SSP_154215
+chr4 56682699 56686499 SSP_154320
+chr4 58146949 58148499 SSP_154376
+chr4 58146299 58148449 SSP_154377
+chr4 58148249 58153649 SSP_154379
+chr4 58148249 58153649 SSP_154380
+chr4 58148249 58157599 SSP_154381
+chr4 58148249 58153649 SSP_154382
+chr4 58148249 58153649 SSP_154383
+chr4 58676999 58678049 SSP_154514
+chr4 59297449 59302149 SSP_154658
+chr1 215583149 215591099 SSP_15526
+chr4 64718899 64722449 SSP_155933
+chr4 67516599 67524049 SSP_156472
+chr4 68999599 69004349 SSP_156664
+chr4 69284349 69292099 SSP_156712
+chr4 70290949 70296849 SSP_156882
+chr4 70290949 70300149 SSP_156883
+chr4 70295049 70300249 SSP_156884
+chr4 70295049 70300249 SSP_156885
+chr4 70295249 70296849 SSP_156886
+chr4 70295649 70300149 SSP_156887
+chr4 80458899 80466649 SSP_157801
+chr4 80458549 80466649 SSP_157804
+chr4 80458549 80466499 SSP_157805
+chr4 92550099 92553049 SSP_158465
+chr4 92545099 92553649 SSP_158466
+chr4 93167749 93173949 SSP_158623
+chr4 93167749 93174049 SSP_158624
+chr4 93171149 93174199 SSP_158626
+chr4 93171149 93174199 SSP_158627
+chr4 93179749 93181099 SSP_158628
+chr4 93180449 93181099 SSP_158629
+chr4 97066099 97073649 SSP_158915
+chr4 107532949 107537099 SSP_159602
+chr4 107534149 107534549 SSP_159603
+chr4 109455799 109464449 SSP_159824
+chr4 111938199 111941049 SSP_159957
+chr4 111938199 111941049 SSP_159958
+chr4 111940799 111941049 SSP_159959
+chr4 116785699 116789099 SSP_160525
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+chr7 89043149 89050799 SSP_213313
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+chr7 115036699 115037249 SSP_215083
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+chr10 36521049 36521649 SSP_22371
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+chr8 66198549 66198799 SSP_224297
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+chr8 86842049 86852099 SSP_226586
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+chr8 93170949 93179849 SSP_226859
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+chr9 787599 799149 SSP_232002
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+chr9 8168849 8172749 SSP_232613
+chr9 8168849 8172749 SSP_232614
+chr9 8168849 8172749 SSP_232615
+chr9 8168849 8172749 SSP_232616
+chr9 12319449 12322349 SSP_233171
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+chr9 14704949 14710749 SSP_233629
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+chr9 20050199 20055299 SSP_234042
+chr9 24907449 24912999 SSP_234718
+chr9 24907549 24909649 SSP_234722
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+chr9 30225449 30229049 SSP_235518
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+chr9 30226349 30227999 SSP_235525
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+chr9 31023299 31031049 SSP_235775
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+chr9 42286249 42297649 SSP_236927
+chr9 43203949 43211949 SSP_237045
+chr9 43203949 43213399 SSP_237046
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+chr10 55236549 55237249 SSP_23729
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+chr9 45394149 45405699 SSP_237291
+chr9 66148449 66151199 SSP_237595
+chr9 70681599 70692999 SSP_237893
+chr9 70686749 70692999 SSP_237894
+chr9 74187349 74188549 SSP_238057
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+chr9 79178349 79187049 SSP_238577
+chr9 79178799 79187049 SSP_238578
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+chr9 85189099 85194149 SSP_239477
+chr9 85189099 85195499 SSP_239478
+chr9 85193499 85195499 SSP_239479
+chr10 58245099 58246599 SSP_23959
+chr9 87274399 87278999 SSP_239720
+chr9 87276449 87277849 SSP_239723
+chr9 89035399 89043799 SSP_239862
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diff --git a/intervene_test/SUNP_filtered_peaks.bed b/intervene_test/SUNP_filtered_peaks.bed
new file mode 100644
index 0000000..b081ebd
--- /dev/null
+++ b/intervene_test/SUNP_filtered_peaks.bed
@@ -0,0 +1,704 @@
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diff --git a/intervene_test/intervene_figure.sh b/intervene_test/intervene_figure.sh
new file mode 100644
index 0000000..69422df
--- /dev/null
+++ b/intervene_test/intervene_figure.sh
@@ -0,0 +1,12 @@
+# Make overlap of enhancer data
+
+
+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 .
+cut -f1,2,3 SUNP_filtered_peaks.bed > t
+cut -f1,2,3 SSP_filtered_peaks_merged.bed >> t
+sort-bed t > GRO-seq_filtered_peaks.bed
+
+intervene upset -i *enhancers.bed --filename --order degree --sxlabel "No. of Unique Enhancers" --dpi 1200 --figsize 10 8 --mbcolor "#108DCC" --sbcolor "#E62128"
--
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