From cd3784bae6565548002c6763a788ad2ce53a5be8 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <Venkat.Malladi@utsouthwestern.edu>
Date: Thu, 23 Feb 2017 16:25:38 -0600
Subject: [PATCH] get 1kb center of enhancer ans figures.
---
ES_D0_gro-seq_enhancers.bed | 1304 ++++++++++++++++++++++
ES_D0_gro-seq_enhancers_1kb.bed | 1304 ++++++++++++++++++++++
ES_D10_gro-seq_enhancers.bed | 1099 ++++++++++++++++++
ES_D10_gro-seq_enhancers_1kb.bed | 1099 ++++++++++++++++++
ES_D2_gro-seq_enhancers.bed | 1535 ++++++++++++++++++++++++++
ES_D2_gro-seq_enhancers_1kb.bed | 1535 ++++++++++++++++++++++++++
ES_D5_gro-seq_enhancers.bed | 651 +++++++++++
ES_D5_gro-seq_enhancers_1kb.bed | 651 +++++++++++
ES_D7_gro-seq_enhancers.bed | 525 +++++++++
ES_D7_gro-seq_enhancers_1kb.bed | 525 +++++++++
Gro_percentages.png | Bin 0 -> 15765 bytes
SSP_filtered_peaks_merged.bed | 1772 ++++++++++++++++++++++--------
SSP_filtered_peaks_sum.tsv | 1306 ++++++++++++++++++++++
gro-seq_enhancer_plots.py | 102 ++
groseq_processing.sh | 37 +-
histone_centered_processing.sh | 69 ++
16 files changed, 13052 insertions(+), 462 deletions(-)
create mode 100644 ES_D0_gro-seq_enhancers.bed
create mode 100644 ES_D0_gro-seq_enhancers_1kb.bed
create mode 100644 ES_D10_gro-seq_enhancers.bed
create mode 100644 ES_D10_gro-seq_enhancers_1kb.bed
create mode 100644 ES_D2_gro-seq_enhancers.bed
create mode 100644 ES_D2_gro-seq_enhancers_1kb.bed
create mode 100644 ES_D5_gro-seq_enhancers.bed
create mode 100644 ES_D5_gro-seq_enhancers_1kb.bed
create mode 100644 ES_D7_gro-seq_enhancers.bed
create mode 100644 ES_D7_gro-seq_enhancers_1kb.bed
create mode 100644 Gro_percentages.png
create mode 100644 SSP_filtered_peaks_sum.tsv
create mode 100644 gro-seq_enhancer_plots.py
diff --git a/ES_D0_gro-seq_enhancers.bed b/ES_D0_gro-seq_enhancers.bed
new file mode 100644
index 0000000..848a072
--- /dev/null
+++ b/ES_D0_gro-seq_enhancers.bed
@@ -0,0 +1,1304 @@
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diff --git a/ES_D0_gro-seq_enhancers_1kb.bed b/ES_D0_gro-seq_enhancers_1kb.bed
new file mode 100644
index 0000000..5e9a354
--- /dev/null
+++ b/ES_D0_gro-seq_enhancers_1kb.bed
@@ -0,0 +1,1304 @@
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diff --git a/ES_D10_gro-seq_enhancers.bed b/ES_D10_gro-seq_enhancers.bed
new file mode 100644
index 0000000..9b16226
--- /dev/null
+++ b/ES_D10_gro-seq_enhancers.bed
@@ -0,0 +1,1099 @@
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diff --git a/ES_D10_gro-seq_enhancers_1kb.bed b/ES_D10_gro-seq_enhancers_1kb.bed
new file mode 100644
index 0000000..c28314a
--- /dev/null
+++ b/ES_D10_gro-seq_enhancers_1kb.bed
@@ -0,0 +1,1099 @@
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diff --git a/ES_D2_gro-seq_enhancers.bed b/ES_D2_gro-seq_enhancers.bed
new file mode 100644
index 0000000..658c340
--- /dev/null
+++ b/ES_D2_gro-seq_enhancers.bed
@@ -0,0 +1,1535 @@
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diff --git a/ES_D2_gro-seq_enhancers_1kb.bed b/ES_D2_gro-seq_enhancers_1kb.bed
new file mode 100644
index 0000000..cdff303
--- /dev/null
+++ b/ES_D2_gro-seq_enhancers_1kb.bed
@@ -0,0 +1,1535 @@
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diff --git a/ES_D5_gro-seq_enhancers.bed b/ES_D5_gro-seq_enhancers.bed
new file mode 100644
index 0000000..2e7b661
--- /dev/null
+++ b/ES_D5_gro-seq_enhancers.bed
@@ -0,0 +1,651 @@
+chr1 25481049 25482049 SSP_1511
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diff --git a/ES_D5_gro-seq_enhancers_1kb.bed b/ES_D5_gro-seq_enhancers_1kb.bed
new file mode 100644
index 0000000..35103f3
--- /dev/null
+++ b/ES_D5_gro-seq_enhancers_1kb.bed
@@ -0,0 +1,651 @@
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diff --git a/ES_D7_gro-seq_enhancers.bed b/ES_D7_gro-seq_enhancers.bed
new file mode 100644
index 0000000..090808c
--- /dev/null
+++ b/ES_D7_gro-seq_enhancers.bed
@@ -0,0 +1,525 @@
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diff --git a/ES_D7_gro-seq_enhancers_1kb.bed b/ES_D7_gro-seq_enhancers_1kb.bed
new file mode 100644
index 0000000..1228e26
--- /dev/null
+++ b/ES_D7_gro-seq_enhancers_1kb.bed
@@ -0,0 +1,525 @@
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diff --git a/Gro_percentages.png b/Gro_percentages.png
new file mode 100644
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literal 0
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diff --git a/SSP_filtered_peaks_merged.bed b/SSP_filtered_peaks_merged.bed
index d5c3547..2369f3e 100644
--- a/SSP_filtered_peaks_merged.bed
+++ b/SSP_filtered_peaks_merged.bed
@@ -1,458 +1,1314 @@
-chr14 84597499 84602349 SSP_10334
-chr14 101755899 101757549 SSP_10633
-chr14 101770749 101778849 SSP_10634
-chr15 78658899 78659799 SSP_11004
-chr15 96286599 96293949 SSP_11163
-chr1 106248799 106250549 SSP_1146
-chr16 34359399 34361899 SSP_11485
-chr16 61088149 61090999 SSP_11781
-chr16 61534699 61546199 SSP_11809
-chr16 61542099 61546199 SSP_11811
-chr16 61542099 61546199 SSP_11812
-chr16 66059249 66063649 SSP_11978
-chr17 12136149 12145399 SSP_12236
-chr17 50252949 50256799 SSP_12390
-chr18 75997399 76001299 SSP_13941
-chr2 35648549 35654349 SSP_14657
-chr2 35661999 35667699 SSP_14658
-chr2 35815699 35821249 SSP_14663
-chr2 76665349 76672599 SSP_15069
-chr2 83286849 83294199 SSP_15219
-chr2 83764949 83767499 SSP_15246
-chr2 104751099 104762599 SSP_15439
-chr2 124112549 124116499 SSP_15725
-chr2 126873249 126881799 SSP_15799
-chr2 126880549 126881799 SSP_15800
-chr2 137060149 137063999 SSP_15968
-chr2 137062399 137063999 SSP_15969
-chr2 143008849 143015849 SSP_16096
-chr2 155420399 155422149 SSP_16370
-chr2 162995249 163003749 SSP_16453
-chr2 162995449 163003749 SSP_16454
-chr2 194211999 194219399 SSP_16784
-chr2 237773099 237778049 SSP_17242
-chr20 4550999 4556349 SSP_17352
-chr20 12744599 12752899 SSP_17470
-chr20 21735349 21737549 SSP_17558
-chr20 22618749 22619149 SSP_17593
-chr20 53739349 53740649 SSP_17848
-chr20 59175849 59176299 SSP_17978
-chr20 59585299 59592599 SSP_18008
-chr21 20230049 20230899 SSP_18165
-chr1 189954199 189961949 SSP_1822
-chr3 13839449 13848399 SSP_18959
-chr3 21003299 21005499 SSP_18991
-chr3 21007349 21014499 SSP_18992
-chr3 21093449 21100149 SSP_18997
-chr3 21093449 21100149 SSP_18998
-chr3 22737649 22743049 SSP_19032
-chr1 193552499 193559499 SSP_1916
-chr3 75263499 75272299 SSP_19582
-chr3 90141849 90148199 SSP_19995
-chr3 90152499 90163099 SSP_19996
-chr3 90172249 90180599 SSP_19997
-chr3 90185999 90189849 SSP_19998
-chr3 90196949 90198649 SSP_19999
-chr3 94381549 94381849 SSP_20029
-chr3 95404799 95406049 SSP_20073
-chr1 195877849 195878199 SSP_2045
-chr3 161680349 161687199 SSP_20851
-chr3 161680349 161687199 SSP_20852
-chr3 162256249 162262399 SSP_20896
-chr3 191612399 191618449 SSP_21243
-chr3 191634949 191640399 SSP_21245
-chr3 191641799 191648249 SSP_21246
-chr4 19079449 19087749 SSP_21488
-chr1 208544149 208548899 SSP_2162
-chr4 58146949 58157599 SSP_22343
-chr4 58146299 58154399 SSP_22344
-chr4 58719649 58720149 SSP_22371
-chr4 60522349 60529949 SSP_22446
-chr4 64199199 64205449 SSP_22591
-chr4 79636499 79640899 SSP_22904
-chr4 97066099 97073649 SSP_23038
-chr4 111938199 111941049 SSP_23232
-chr4 125179499 125182949 SSP_23464
-chr4 125179499 125184299 SSP_23465
-chr4 134211749 134211899 SSP_23723
-chr4 134226649 134228199 SSP_23724
-chr4 134239949 134248949 SSP_23725
-chr4 134265699 134271599 SSP_23726
-chr4 134283799 134291449 SSP_23727
-chr4 134318149 134319099 SSP_23728
-chr4 134361649 134367399 SSP_23731
-chr4 134374549 134377999 SSP_23732
-chr4 134374549 134383799 SSP_23733
-chr4 134377799 134383799 SSP_23734
-chr4 136908899 136918399 SSP_23827
-chr4 136914249 136918399 SSP_23829
-chr1 30781999 30785999 SSP_240
-chr4 165656549 165664399 SSP_24333
-chr4 179493199 179502299 SSP_24588
-chr5 18953599 18956699 SSP_25228
-chr5 26590999 26593449 SSP_25415
-chr5 28617049 28623249 SSP_25535
-chr5 34600599 34608349 SSP_25708
-chr5 34601299 34616549 SSP_25710
-chr5 57318899 57324099 SSP_26088
-chr5 66597049 66601149 SSP_26223
-chr5 66597099 66601149 SSP_26224
-chr5 71711549 71718949 SSP_26277
-chr5 71711549 71720599 SSP_26278
-chr5 84382799 84389599 SSP_26371
-chr5 86197899 86200049 SSP_26463
-chr5 119768849 119774699 SSP_26980
-chr5 143352799 143355299 SSP_27234
-chr5 143352799 143355299 SSP_27235
-chr5 146474499 146480149 SSP_27268
-chr5 146492349 146494749 SSP_27269
-chr5 161691149 161697299 SSP_27413
-chr5 174537199 174543149 SSP_27574
-chr6 18833499 18841599 SSP_27799
-chr6 18936499 18942799 SSP_27806
-chr6 58146799 58154349 SSP_28325
-chr10 9544699 9553099 SSP_2834
-chr6 58706849 58707249 SSP_28348
-chr6 58706849 58707249 SSP_28348
-chr6 63518249 63520149 SSP_28384
-chr6 63604199 63609249 SSP_28385
-chr6 85389649 85397749 SSP_28731
-chr6 87304749 87312049 SSP_28769
-chr10 10274549 10283099 SSP_2877
-chr6 113371399 113375449 SSP_29229
-chr6 122531749 122535449 SSP_29394
-chr6 133341799 133347649 SSP_29482
-chr6 137735049 137736949 SSP_29529
-chr6 142966699 142973249 SSP_29661
-chr7 8953399 8958999 SSP_30052
-chr7 8953399 8958999 SSP_30053
-chr7 9242799 9246749 SSP_30066
-chr7 20503999 20508549 SSP_30212
-chr7 45289199 45294349 SSP_30410
-chr7 80959599 80966199 SSP_30926
-chr7 80959599 80966199 SSP_30927
-chr10 37260849 37268749 SSP_3099
-chr7 89043149 89050799 SSP_31097
-chr7 115032699 115037249 SSP_31310
-chr7 118158999 118162899 SSP_31382
-chr7 118158999 118169199 SSP_31383
-chr7 118339799 118344199 SSP_31393
-chr7 137926649 137934449 SSP_31617
-chr7 155962149 155967449 SSP_31738
-chr8 305549 310899 SSP_31761
-chr8 4886499 4892699 SSP_31803
-chr1 37227249 37233349 SSP_322
-chr8 55107549 55112999 SSP_32430
-chr8 57500899 57501399 SSP_32461
-chr8 86845749 86852049 SSP_32986
-chr8 92448349 92455749 SSP_33017
-chr8 93170949 93183399 SSP_33026
-chr8 116224849 116233849 SSP_33309
-chr8 116224849 116233849 SSP_33310
-chr8 127243649 127249149 SSP_33470
-chr8 132530749 132536599 SSP_33553
-chr8 137027649 137034649 SSP_33651
-chr8 137029849 137039399 SSP_33652
-chr10 59386849 59390549 SSP_3370
-chr8 140597099 140603149 SSP_33709
-chr8 140597099 140603149 SSP_33709
-chr1 37791749 37795699 SSP_338
-chr9 6146049 6148499 SSP_33826
-chr9 8168649 8175899 SSP_33869
-chr9 6146049 6148499 SSP_33826
-chr9 8168649 8175899 SSP_33869
-chr9 12319449 12322349 SSP_33982
-chr9 20048949 20055899 SSP_34108
-chr9 24500749 24504199 SSP_34193
-chr9 30225499 30229049 SSP_34366
-chr9 30225499 30229049 SSP_34367
-chr10 64060899 64064399 SSP_3457
-chr9 105719549 105724699 SSP_35011
-chr10 66457249 66465699 SSP_3506
-chr10 66830899 66831799 SSP_3525
-chrX 38832049 38836599 SSP_35880
-chrX 39554399 39562499 SSP_35910
-chrX 42586999 42593749 SSP_35950
-chrX 72200699 72206399 SSP_36232
-chrX 97777549 97784749 SSP_36870
-chrX 110785149 110792949 SSP_37036
-chrX 137322699 137325949 SSP_37321
-chrX 137343599 137352499 SSP_37322
-chr10 90527349 90532949 SSP_3758
-chr10 90527349 90532949 SSP_3759
-chrY 3547249 3555799 SSP_37802
-chrY 5844899 5847799 SSP_37889
-chrY 17346199 17355499 SSP_38109
-chrY 18647349 18654899 SSP_38149
-chrY 25204449 25209849 SSP_38327
-chrY 26838249 26841699 SSP_38380
-chr10 126000449 126008499 SSP_4217
-chr10 126000449 126008499 SSP_4218
-chr11 15549149 15556749 SSP_4560
-chr11 21614199 21620649 SSP_4614
-chr11 96953949 96959399 SSP_5600
-chr11 97140249 97143249 SSP_5607
-chr11 97246249 97253149 SSP_5615
-chr1 74236749 74243749 SSP_586
-chr11 121258499 121262449 SSP_5965
-chr1 74487749 74489349 SSP_601
-chr1 75540599 75541049 SSP_621
-chr1 77164149 77168399 SSP_629
-chr12 55504749 55506749 SSP_6571
-chr12 60536249 60538299 SSP_6628
-chr12 85229399 85237949 SSP_6986
-chr1 81709999 81717799 SSP_719
-chr12 127317349 127320699 SSP_7442
-chr12 127341749 127351649 SSP_7443
-chr13 19254699 19257499 SSP_7562
-chr13 37163549 37165499 SSP_7735
-chr13 54515149 54517299 SSP_7946
-chr13 54657749 54664749 SSP_7961
-chr13 54657799 54664749 SSP_7962
-chr13 54666699 54669699 SSP_7963
-chr13 54674549 54683049 SSP_7964
-chr1 88227249 88229049 SSP_800
-chr13 57974349 57980849 SSP_8058
-chr13 58137049 58138999 SSP_8074
-chr13 58346249 58352399 SSP_8079
-chr13 61606899 61613749 SSP_8154
-chr13 61662099 61668599 SSP_8156
-chr13 61673049 61675599 SSP_8157
-chr13 66057399 66058699 SSP_8409
-chr13 80312549 80313299 SSP_8851
-chr13 86520099 86526599 SSP_9050
-chr13 87998899 88000249 SSP_9113
-chr13 89855049 89861149 SSP_9232
-chr13 105414149 105423599 SSP_9552
-chr13 105703949 105712299 SSP_9572
-chr13 112187149 112187399 SSP_9738
-chr13 112214349 112220699 SSP_9741
-chr14 84597499 84602349 SSP_10334
-chr14 101755899 101757549 SSP_10633
-chr14 101770749 101778849 SSP_10634
-chr15 78658899 78659799 SSP_11004
-chr15 96286599 96293949 SSP_11163
-chr1 106248799 106250549 SSP_1146
-chr16 34359399 34361899 SSP_11485
-chr16 61088149 61090999 SSP_11781
-chr16 61534699 61546199 SSP_11809
-chr16 61542099 61546199 SSP_11811
-chr16 61542099 61546199 SSP_11812
-chr16 66059249 66063649 SSP_11978
-chr17 12136149 12145399 SSP_12236
-chr17 50252949 50256799 SSP_12390
-chr18 75997399 76001299 SSP_13941
-chr2 35648549 35654349 SSP_14657
-chr2 35661999 35667699 SSP_14658
-chr2 35815699 35821249 SSP_14663
-chr2 76665349 76672599 SSP_15069
-chr2 83286849 83294199 SSP_15219
-chr2 83764949 83767499 SSP_15246
-chr2 104751099 104762599 SSP_15439
-chr2 124112549 124116499 SSP_15725
-chr2 126873249 126881799 SSP_15799
-chr2 126880549 126881799 SSP_15800
-chr2 137060149 137063999 SSP_15968
-chr2 137062399 137063999 SSP_15969
-chr2 143008849 143015849 SSP_16096
-chr2 155420399 155422149 SSP_16370
-chr2 162995249 163003749 SSP_16453
-chr2 162995449 163003749 SSP_16454
-chr2 194211999 194219399 SSP_16784
-chr2 237773099 237778049 SSP_17242
-chr20 4550999 4556349 SSP_17352
-chr20 12744599 12752899 SSP_17470
-chr20 21735349 21737549 SSP_17558
-chr20 22618749 22619149 SSP_17593
-chr20 53739349 53740649 SSP_17848
-chr20 59175849 59176299 SSP_17978
-chr20 59585299 59592599 SSP_18008
-chr21 20230049 20230899 SSP_18165
-chr1 189954199 189961949 SSP_1822
-chr3 13839449 13848399 SSP_18959
-chr3 21003299 21005499 SSP_18991
-chr3 21007349 21014499 SSP_18992
-chr3 21093449 21100149 SSP_18997
-chr3 21093449 21100149 SSP_18998
-chr3 22737649 22743049 SSP_19032
-chr1 193552499 193559499 SSP_1916
-chr3 75263499 75272299 SSP_19582
-chr3 90141849 90148199 SSP_19995
-chr3 90152499 90163099 SSP_19996
-chr3 90172249 90180599 SSP_19997
-chr3 90185999 90189849 SSP_19998
-chr3 90196949 90198649 SSP_19999
-chr3 94381549 94381849 SSP_20029
-chr3 95404799 95406049 SSP_20073
-chr1 195877849 195878199 SSP_2045
-chr3 161680349 161687199 SSP_20851
-chr3 161680349 161687199 SSP_20852
-chr3 162256249 162262399 SSP_20896
-chr3 191612399 191618449 SSP_21243
-chr3 191634949 191640399 SSP_21245
-chr3 191641799 191648249 SSP_21246
-chr4 19079449 19087749 SSP_21488
-chr1 208544149 208548899 SSP_2162
-chr4 58146949 58157599 SSP_22343
-chr4 58146299 58154399 SSP_22344
-chr4 58719649 58720149 SSP_22371
-chr4 60522349 60529949 SSP_22446
-chr4 64199199 64205449 SSP_22591
-chr4 79636499 79640899 SSP_22904
-chr4 97066099 97073649 SSP_23038
-chr4 111938199 111941049 SSP_23232
-chr4 125179499 125182949 SSP_23464
-chr4 125179499 125184299 SSP_23465
-chr4 134211749 134211899 SSP_23723
-chr4 134226649 134228199 SSP_23724
-chr4 134239949 134248949 SSP_23725
-chr4 134265699 134271599 SSP_23726
-chr4 134283799 134291449 SSP_23727
-chr4 134318149 134319099 SSP_23728
-chr4 134361649 134367399 SSP_23731
-chr4 134374549 134377999 SSP_23732
-chr4 134374549 134383799 SSP_23733
-chr4 134377799 134383799 SSP_23734
-chr4 136908899 136918399 SSP_23827
-chr4 136914249 136918399 SSP_23829
-chr1 30781999 30785999 SSP_240
-chr4 165656549 165664399 SSP_24333
-chr4 179493199 179502299 SSP_24588
-chr5 18953599 18956699 SSP_25228
-chr5 26590999 26593449 SSP_25415
-chr5 28617049 28623249 SSP_25535
-chr5 34600599 34608349 SSP_25708
-chr5 34601299 34616549 SSP_25710
-chr5 57318899 57324099 SSP_26088
-chr5 66597049 66601149 SSP_26223
-chr5 66597099 66601149 SSP_26224
-chr5 71711549 71718949 SSP_26277
-chr5 71711549 71720599 SSP_26278
-chr5 84382799 84389599 SSP_26371
-chr5 86197899 86200049 SSP_26463
-chr5 119768849 119774699 SSP_26980
-chr5 143352799 143355299 SSP_27234
-chr5 143352799 143355299 SSP_27235
-chr5 146474499 146480149 SSP_27268
-chr5 146492349 146494749 SSP_27269
-chr5 161691149 161697299 SSP_27413
-chr5 174537199 174543149 SSP_27574
-chr6 18833499 18841599 SSP_27799
-chr6 18936499 18942799 SSP_27806
-chr6 58146799 58154349 SSP_28325
-chr10 9544699 9553099 SSP_2834
-chr6 58706849 58707249 SSP_28348
-chr6 58706849 58707249 SSP_28348
-chr6 63518249 63520149 SSP_28384
-chr6 63604199 63609249 SSP_28385
-chr6 85389649 85397749 SSP_28731
-chr6 87304749 87312049 SSP_28769
-chr10 10274549 10283099 SSP_2877
-chr6 113371399 113375449 SSP_29229
-chr6 122531749 122535449 SSP_29394
-chr6 133341799 133347649 SSP_29482
-chr6 137735049 137736949 SSP_29529
-chr6 142966699 142973249 SSP_29661
-chr7 8953399 8958999 SSP_30052
-chr7 8953399 8958999 SSP_30053
-chr7 9242799 9246749 SSP_30066
-chr7 20503999 20508549 SSP_30212
-chr7 45289199 45294349 SSP_30410
-chr7 80959599 80966199 SSP_30926
-chr7 80959599 80966199 SSP_30927
-chr10 37260849 37268749 SSP_3099
-chr7 89043149 89050799 SSP_31097
-chr7 115032699 115037249 SSP_31310
-chr7 118158999 118162899 SSP_31382
-chr7 118158999 118169199 SSP_31383
-chr7 118339799 118344199 SSP_31393
-chr7 137926649 137934449 SSP_31617
-chr7 155962149 155967449 SSP_31738
-chr8 305549 310899 SSP_31761
-chr8 4886499 4892699 SSP_31803
-chr1 37227249 37233349 SSP_322
-chr8 55107549 55112999 SSP_32430
-chr8 57500899 57501399 SSP_32461
-chr8 86845749 86852049 SSP_32986
-chr8 92448349 92455749 SSP_33017
-chr8 93170949 93183399 SSP_33026
-chr8 116224849 116233849 SSP_33309
-chr8 116224849 116233849 SSP_33310
-chr8 127243649 127249149 SSP_33470
-chr8 132530749 132536599 SSP_33553
-chr8 137027649 137034649 SSP_33651
-chr8 137029849 137039399 SSP_33652
-chr10 59386849 59390549 SSP_3370
-chr8 140597099 140603149 SSP_33709
-chr8 140597099 140603149 SSP_33709
-chr1 37791749 37795699 SSP_338
-chr9 6146049 6148499 SSP_33826
-chr9 8168649 8175899 SSP_33869
-chr9 6146049 6148499 SSP_33826
-chr9 8168649 8175899 SSP_33869
-chr9 12319449 12322349 SSP_33982
-chr9 20048949 20055899 SSP_34108
-chr9 24500749 24504199 SSP_34193
-chr9 30225499 30229049 SSP_34366
-chr9 30225499 30229049 SSP_34367
-chr10 64060899 64064399 SSP_3457
-chr9 105719549 105724699 SSP_35011
-chr10 66457249 66465699 SSP_3506
-chr10 66830899 66831799 SSP_3525
-chrX 38832049 38836599 SSP_35880
-chrX 39554399 39562499 SSP_35910
-chrX 42586999 42593749 SSP_35950
-chrX 72200699 72206399 SSP_36232
-chrX 97777549 97784749 SSP_36870
-chrX 110785149 110792949 SSP_37036
-chrX 137322699 137325949 SSP_37321
-chrX 137343599 137352499 SSP_37322
-chr10 90527349 90532949 SSP_3758
-chr10 90527349 90532949 SSP_3759
-chrY 3547249 3555799 SSP_37802
-chrY 5844899 5847799 SSP_37889
-chrY 17346199 17355499 SSP_38109
-chrY 18647349 18654899 SSP_38149
-chrY 25204449 25209849 SSP_38327
-chrY 26838249 26841699 SSP_38380
-chr10 126000449 126008499 SSP_4217
-chr10 126000449 126008499 SSP_4218
-chr11 15549149 15556749 SSP_4560
-chr11 21614199 21620649 SSP_4614
-chr11 96953949 96959399 SSP_5600
-chr11 97140249 97143249 SSP_5607
-chr11 97246249 97253149 SSP_5615
-chr1 74236749 74243749 SSP_586
-chr11 121258499 121262449 SSP_5965
-chr1 74487749 74489349 SSP_601
-chr1 75540599 75541049 SSP_621
-chr1 77164149 77168399 SSP_629
-chr12 55504749 55506749 SSP_6571
-chr12 60536249 60538299 SSP_6628
-chr12 85229399 85237949 SSP_6986
-chr1 81709999 81717799 SSP_719
-chr12 127317349 127320699 SSP_7442
-chr12 127341749 127351649 SSP_7443
-chr13 19254699 19257499 SSP_7562
-chr13 37163549 37165499 SSP_7735
-chr13 54515149 54517299 SSP_7946
-chr13 54657749 54664749 SSP_7961
-chr13 54657799 54664749 SSP_7962
-chr13 54666699 54669699 SSP_7963
-chr13 54674549 54683049 SSP_7964
-chr1 88227249 88229049 SSP_800
-chr13 57974349 57980849 SSP_8058
-chr13 58137049 58138999 SSP_8074
-chr13 58346249 58352399 SSP_8079
-chr13 61606899 61613749 SSP_8154
-chr13 61662099 61668599 SSP_8156
-chr13 61673049 61675599 SSP_8157
-chr13 66057399 66058699 SSP_8409
-chr13 80312549 80313299 SSP_8851
-chr13 86520099 86526599 SSP_9050
-chr13 87998899 88000249 SSP_9113
-chr13 89855049 89861149 SSP_9232
-chr13 105414149 105423599 SSP_9552
-chr13 105703949 105712299 SSP_9572
-chr13 112187149 112187399 SSP_9738
-chr13 112214349 112220699 SSP_9741
+chr2 14536049 14542999 SSP_100925
+chr1 160595699 160600699 SSP_10167
+chr1 160621649 160622949 SSP_10168
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+chrY 26834599 26841749 SSP_266997
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+chr10 94957999 94960099 SSP_27458
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+chr13 57974349 57980949 SSP_57058
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+chr13 58346249 58352399 SSP_57134
+chr13 61662099 61668149 SSP_57843
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+chr15 20384399 20385849 SSP_73324
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+chr18 4548449 4548749 SSP_89330
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+chr18 60725299 60731249 SSP_94648
+chr18 62590899 62593599 SSP_94899
+chr18 62590899 62591599 SSP_94904
+chr18 62720399 62729149 SSP_94939
+chr18 62722049 62725849 SSP_94942
+chr18 70701649 70707849 SSP_96571
+chr18 70970149 70975299 SSP_96599
+chr18 73350299 73353399 SSP_96854
+chr18 73457199 73463749 SSP_96877
+chr18 73460699 73463799 SSP_96878
+chr18 75997399 75997699 SSP_97295
+chr19 27731899 27732799 SSP_97822
+chr19 27731949 27732799 SSP_97823
+chr19 27731949 27739449 SSP_97824
+chr19 27737199 27742799 SSP_97825
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+chr19 52158899 52166649 SSP_99025
diff --git a/SSP_filtered_peaks_sum.tsv b/SSP_filtered_peaks_sum.tsv
new file mode 100644
index 0000000..d40aad6
--- /dev/null
+++ b/SSP_filtered_peaks_sum.tsv
@@ -0,0 +1,1306 @@
+ name ES_D0 ES_D2 ES_D5 ES_D7 ES_D10
+1031 SSP_100925 0.00145903588054 0.002310816901 0.0 0.000790661968333 0.792536672005
+1858 SSP_10167 0.00556712891794 0.521224399775 0.0 0.00124183066213 0.00520945448023
+1869 SSP_10168 0.395258941867 0.761005332044 0.0114415255826 0.0270528033473 0.0399391510151
+1880 SSP_10169 0.264262347211 0.568377328082 0.00317311642824 0.0141651484193 0.0240792562641
+2441 SSP_102194 0.240108568586 0.505815555945 0.0594959330295 0.0366340045328 0.0376238379128
+2442 SSP_102195 0.239894185936 0.505281995232 0.0594959330295 0.0366340045328 0.0376238379128
+2537 SSP_102280 0.232402076465 0.850505137271 0.00156568244815 0.000642701833909 0.00297030299312
+3722 SSP_103347 0.240908930482 0.964375418074 0.0 0.109902013598 0.0583169487648
+3825 SSP_10344 0.0662893356857 0.537269737008 0.0 0.0 0.0
+4932 SSP_104436 0.983529373214 0.438468337057 0.00403984730447 0.0027136299654 0.00209021321737
+4933 SSP_104437 2.22487649913 0.568999290574 0.00523480892235 0.0013568149827 0.000696737739125
+4994 SSP_104492 0.256691336834 0.160023376872 2.26054547563 0.00153924388793 0.012709901547
+4995 SSP_104493 0.259564177781 0.160448249292 2.25994736836 0.00255685512495 0.0105301077632
+5110 SSP_104597 0.55210125627 0.157278665338 0.00790918157339 0.00287111741874 0.00358322265837
+5111 SSP_104598 1.14180429364 0.206733814982 0.00786196257892 0.00333631112709 0.00161245019626
+5112 SSP_104599 1.05077206066 0.11209348351 0.000424970950211 0.0010466858438 0.00161245019626
+5199 SSP_104677 0.0 0.0 0.0 0.0 0.940595947819
+5881 SSP_105290 0.220413566593 0.329691201295 0.57492117354 0.645557904271 0.959146455653
+5882 SSP_105291 0.220283482575 0.330438331085 0.574574046658 0.646010237298 0.960540120205
+5883 SSP_105292 0.221970040632 0.333436578501 0.575892422447 0.646155940725 0.960989040999
+6131 SSP_105515 3.94589609467 4.47771608206 1.14829197199 1.15086103264 2.8485233568
+6433 SSP_105788 0.0321864664124 0.658220993962 0.0201681128913 0.000206971777021 0.0
+6512 SSP_105859 0.00824295619762 0.91614632884 0.00220355307516 0.0 0.0
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+253113 SSP_87202 0.319573071046 1.59072233909 0.0198319776765 0.0158747352975 0.112871513738
+253602 SSP_87643 0.0678160334652 0.111060478429 0.000594959330295 0.0023622616716 2.96026951445
+253603 SSP_87644 0.0867875539446 0.144791885638 0.00329931992254 0.0027642021602 3.9014551776
+254637 SSP_88575 0.219412280367 0.443566806093 0.118991866059 0.0252021165935 1.69307270608
+254939 SSP_88847 0.201511615434 0.975082203048 0.096680891173 0.0686887584989 0.112871513738
+254940 SSP_88848 0.200501373902 0.975082203048 0.096680891173 0.0686887584989 0.112871513738
+254941 SSP_88849 0.529534935954 2.60021920813 0.257815709795 0.183170022664 0.225743027476
+254943 SSP_88850 0.528524694423 2.60021920813 0.257815709795 0.183170022664 0.225743027476
+255477 SSP_89330 0.0676019957983 0.711236430459 0.0297479665148 0.0366340045328 0.112871513738
+255510 SSP_89360 0.38386587824 0.856542797971 0.0594959330295 0.00281800034868 0.0752476758256
+255513 SSP_89363 0.381725163239 0.856975686852 0.0594959330295 0.000345603816347 0.0944145366492
+259352 SSP_92818 0.0273418090613 0.0472909015644 0.00182130407233 0.0301545207378 0.5301889812
+259702 SSP_93132 0.166195555904 0.184200402728 0.161205647113 0.0143047065318 14.9382761016
+259703 SSP_93133 0.00948183837171 0.0104882791588 0.0110492447055 0.00274755033996 0.801790860092
+259705 SSP_93135 0.0092184539725 0.0103923497763 0.00849941900424 0.00199444711089 0.80430785552
+261385 SSP_94648 1.04790840087 0.837519938714 0.00149989747133 0.0137505787322 1.48345418057
+261663 SSP_94899 0.00862454797426 0.0017994596596 0.00116658692215 0.00667005684769 0.679442249366
+261670 SSP_94904 0.00790153197642 0.0 0.0 0.00889682967223 0.688516233804
+261708 SSP_94939 0.000105353759686 0.000524413957942 0.0 0.000209337168759 1.07227938051
+261712 SSP_94942 0.000242590894013 0.0 0.0 0.000482026375433 1.07227938051
+263522 SSP_96571 0.0933740176569 0.597631027675 0.000479805911528 0.0 0.00546152485831
+263552 SSP_96599 0.602809323521 0.780065762439 0.0991598883828 0.0247783396355 0.52673373078
+263836 SSP_96854 0.989348269886 0.0710496330115 0.0 0.0 0.0
+263861 SSP_96877 0.000422219265916 0.0156456836053 0.0 0.0 0.52673373078
+263862 SSP_96878 0.0 0.016060177462 0.0 0.0 0.52673373078
+264326 SSP_97295 1.65624889706 4.80275783149 0.188403787927 0.00610566742212 0.658417163474
+264912 SSP_97822 5.45370967173 0.391382475965 0.0174988038322 0.040943887419 0.745837257448
+264913 SSP_97823 5.41990867383 0.414325586625 0.0174988038322 0.040943887419 0.783461095361
+264914 SSP_97824 5.3759199438 0.341800720042 0.0174988038322 0.0416814848257 0.67513474325
+264915 SSP_97825 1.1238283084 0.0674636706311 0.00159364106329 0.0065417865237 0.127988234328
+264916 SSP_97826 1.13844260719 0.0921738920833 0.00159364106329 0.00597102662566 0.132533395955
+266249 SSP_99025 0.0142142612866 0.000592080275096 0.625858830998 0.000472696832682 0.057892163498
diff --git a/gro-seq_enhancer_plots.py b/gro-seq_enhancer_plots.py
new file mode 100644
index 0000000..40da530
--- /dev/null
+++ b/gro-seq_enhancer_plots.py
@@ -0,0 +1,102 @@
+import pandas as pd
+import matplotlib.pyplot as plt
+import numpy as np
+
+
+ssp_file = pd.read_csv("SSP_sum.tsv", sep='\t')
+
+ssp_file_filtered = pd.read_csv("SSP_filtered_peaks.tsv" , sep='\t')
+sunp_potential_enhancers = pd.read_csv("SUNP_filtered_peaks.tsv" , sep='\t')
+
+
+named_enhancers = list(ssp_file_filtered['name'])
+ssp_potential_enhancers = ssp_file[ssp_file['name'].isin(named_enhancers)]
+ssp_potential_enhancers.to_csv('SSP_filtered_peaks_sum.tsv', header=True, index=True, sep='\t')
+
+# get numbers for each
+es_d0_none = len(ssp_potential_enhancers[ssp_potential_enhancers['ES_D0'] < 0.5 ]) + len(sunp_potential_enhancers[sunp_potential_enhancers['ES_D0'] < 1])
+es_d0_enhancers = len(ssp_potential_enhancers[ssp_potential_enhancers['ES_D0'] >= 0.5 ]) + len(sunp_potential_enhancers[sunp_potential_enhancers['ES_D0'] >= 1])
+
+es_d2_none = len(ssp_potential_enhancers[ssp_potential_enhancers['ES_D2'] < 0.5 ]) + len(sunp_potential_enhancers[sunp_potential_enhancers['ES_D2'] < 1])
+es_d2_enhancers = len(ssp_potential_enhancers[ssp_potential_enhancers['ES_D2'] >= 0.5 ]) + len(sunp_potential_enhancers[sunp_potential_enhancers['ES_D2'] >= 1])
+
+es_d5_none = len(ssp_potential_enhancers[ssp_potential_enhancers['ES_D5'] < 0.5 ]) + len(sunp_potential_enhancers[sunp_potential_enhancers['ES_D5'] < 1])
+es_d5_enhancers = len(ssp_potential_enhancers[ssp_potential_enhancers['ES_D5'] >= 0.5 ]) + len(sunp_potential_enhancers[sunp_potential_enhancers['ES_D5'] >= 1])
+
+es_d7_none = len(ssp_potential_enhancers[ssp_potential_enhancers['ES_D7'] < 0.5 ]) + len(sunp_potential_enhancers[sunp_potential_enhancers['ES_D7'] < 1])
+es_d7_enhancers = len(ssp_potential_enhancers[ssp_potential_enhancers['ES_D7'] >= 0.5 ]) + len(sunp_potential_enhancers[sunp_potential_enhancers['ES_D7'] >= 1])
+
+es_d10_none = len(ssp_potential_enhancers[ssp_potential_enhancers['ES_D10'] < 0.5 ]) + len(sunp_potential_enhancers[sunp_potential_enhancers['ES_D10'] < 1])
+es_d10_enhancers = len(ssp_potential_enhancers[ssp_potential_enhancers['ES_D10'] >= 0.5 ]) + len(sunp_potential_enhancers[sunp_potential_enhancers['ES_D10'] >= 1])
+
+raw_data = {'Cell': ['hES', 'DE', 'GT', 'FG', 'PE'],
+ 'unmarked': [float(es_d0_none),float(es_d2_none),float(es_d5_none),float(es_d7_none),float(es_d10_none)],
+ 'GRO-seq': [es_d0_enhancers,es_d2_enhancers ,es_d5_enhancers,es_d7_enhancers,es_d10_enhancers]}
+
+df = pd.DataFrame(raw_data, columns = ['Cell', 'unmarked', 'GRO-seq'])
+
+# Create a figure with a single subplot
+f, ax = plt.subplots(1, figsize=(10,5))
+
+# Set bar width at 1
+bar_width = 1
+
+# positions of the left bar-boundaries
+bar_l = [i for i in range(len(df['unmarked']))]
+
+# positions of the x-axis ticks (center of the bars as bar labels)
+tick_pos = [i+(bar_width/2) for i in bar_l]
+
+# Create the total enhancers
+totals = [i+j for i,j in zip(df['unmarked'], df['GRO-seq''])]
+
+# Create the percentage of the total unmarked enhancers value for each cell was
+unmarked_rel = [i / float(j) * 100 for i,j in zip(df['unmarked'], totals)]
+
+# Create the percentage of the total H3K4me1 alone enhancers value for each cell
+alone_rel = [i / float(j) * 100 for i,j in zip(df['GRO-seq'], totals)]
+
+
+
+N = 5
+ind = np.arange(N) # the x locations for the groups
+width = 0.5 # the width of the bars: can also be len(x) sequence
+
+p1 = plt.bar(ind, alone_rel, width, color='#E62128')
+p2 = plt.bar(ind, unmarked_rel, width,
+ bottom=alone_rel,color='#D2D5D4')
+
+plt.ylabel('% total enhancers')
+plt.title('Stage')
+plt.xticks(ind, ('hES', 'DE', 'GT', 'FG', 'PE'))
+plt.yticks(np.arange(0, 110, 10))
+
+plt.savefig('Gro_percentages.png')
+plt.clf()
+
+
+
+# Get 1kb centered files
+short_short = pd.read_csv("short_short_paired_1kb.bed", sep='\t', header=None, names= ['chr', 'start', 'end', 'name', 'score', 'strand'])
+short_unpaired = pd.read_csv("short_unpaired_1kb.bed", sep='\t', header=None, names= ['chr', 'start', 'end', 'name', 'score', 'strand'])
+universe_enhancers = pd.concat([short_short,short_unpaired])
+
+es_d0_names = list(ssp_potential_enhancers[ssp_potential_enhancers['ES_D0'] >= 0.5 ]['name']) + list(sunp_potential_enhancers[sunp_potential_enhancers['ES_D0'] >= 1 ]['name'])
+es_d2_names = list(ssp_potential_enhancers[ssp_potential_enhancers['ES_D2'] >= 0.5 ]['name']) + list(sunp_potential_enhancers[sunp_potential_enhancers['ES_D2'] >= 1 ]['name'])
+es_d5_names = list(ssp_potential_enhancers[ssp_potential_enhancers['ES_D5'] >= 0.5 ]['name']) + list(sunp_potential_enhancers[sunp_potential_enhancers['ES_D5'] >= 1 ]['name'])
+es_d7_names = list(ssp_potential_enhancers[ssp_potential_enhancers['ES_D7'] >= 0.5 ]['name']) + list(sunp_potential_enhancers[sunp_potential_enhancers['ES_D7'] >= 1 ]['name'])
+es_d10_names = list(ssp_potential_enhancers[ssp_potential_enhancers['ES_D10'] >= 0.5 ]['name']) + list(sunp_potential_enhancers[sunp_potential_enhancers['ES_D10'] >= 1 ]['name'])
+
+
+es_d0_enhancers = universe_enhancers[universe_enhancers['name'].isin(es_d0_names)]
+es_d2_enhancers = universe_enhancers[universe_enhancers['name'].isin(es_d2_names)]
+es_d5_enhancers = universe_enhancers[universe_enhancers['name'].isin(es_d5_names)]
+es_d7_enhancers = universe_enhancers[universe_enhancers['name'].isin(es_d7_names)]
+es_d10_enhancers = universe_enhancers[universe_enhancers['name'].isin(es_d10_names)]
+
+
+es_d0_enhancers.to_csv("ES_D0_gro-seq_enhancers.bed", index_label="gene_id",sep='\t', columns=["chr", "start", "end","name"],header=False,index=False)
+es_d2_enhancers.to_csv("ES_D2_gro-seq_enhancers.bed", index_label="gene_id",sep='\t', columns=["chr", "start", "end","name"],header=False,index=False)
+es_d5_enhancers.to_csv("ES_D5_gro-seq_enhancers.bed", index_label="gene_id",sep='\t', columns=["chr", "start", "end","name"],header=False,index=False)
+es_d7_enhancers.to_csv("ES_D7_gro-seq_enhancers.bed", index_label="gene_id",sep='\t', columns=["chr", "start", "end","name"],header=False,index=False)
+es_d10_enhancers.to_csv("ES_D10_gro-seq_enhancers.bed", index_label="gene_id",sep='\t', columns=["chr", "start", "end","name"],header=False,index=False)
diff --git a/groseq_processing.sh b/groseq_processing.sh
index d565f0b..f3ef14a 100644
--- a/groseq_processing.sh
+++ b/groseq_processing.sh
@@ -70,8 +70,37 @@ bedtools intersect -a /Volumes/project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT
./cutoff_analysis_gro.py --rpkm SUNP_sum.tsv --color '#FF7C21' --factor SUNP -l 1
# Filter SSP Paired and merge
-cut -f4 SSP_filtered_peaks.bed | sort -u > t
-for i in $(cat t); do grep $i short_short_paired_1kb.bed >> gro_seq_potential_enhancers.bed; done
-cut -f4 SUNP_filtered_peaks.bed | sort -u > t
-for i in $(cat t); do grep $i short_unpaired_1kb.bed >> gro_seq_potential_enhancers.bed; done
for i in $(cat t); do grep $i SSP_filtered_peaks.bed > tt; bedtools merge -c 4 -o distinct -i tt >> SSP_filtered_peaks_merged.bed; done
+
+
+# Acutal Processing
+python gro-seq_enhancer_plots.py
+
+
+bedtools sort -i ES_D0_gro-seq_enhancers.bed > ES_D0_gro-seq_enhancers_1kb.bed
+bedtools sort -i ES_D2_gro-seq_enhancers.bed > ES_D2_gro-seq_enhancers_1kb.bed
+bedtools sort -i ES_D5_gro-seq_enhancers.bed > ES_D5_gro-seq_enhancers_1kb.bed
+bedtools sort -i ES_D7_gro-seq_enhancers.bed > ES_D7_gro-seq_enhancers_1kb.bed
+bedtools sort -i ES_D10_gro-seq_enhancers.bed > ES_D10_gro-seq_enhancers_1kb.bed
+
+
+# Meme processing
+#!/bin/bash
+
+#SBATCH --job-name=fasta_processing
+#SBATCH --partition=super
+#SBATCH --nodes=2
+#SBATCH --ntasks=64
+#SBATCH --time=0-36:00:00
+#SBATCH --output=fasta_processing.%j.out
+#SBATCH --error=fasta_processing.%j.err
+#SBATCH --mail-user=venkat.malladi@utsouthwestern.edu
+#SBATCH --mail-type=ALL
+# Fasta file processing
+
+module load bedtools
+bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D0_gro-seq_enhancers_1kb.bed -fo ES_D0_gro-seq_enhancers.fasta -name
+bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D2_gro-seq_enhancers_1kb.bed -fo ES_D2_gro-seq_enhancers.fasta -name
+bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D5_gro-seq_enhancers_1kb.bed -fo ES_D5_gro-seq_enhancers.fasta -name
+bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D7_gro-seq_enhancers_1kb.bed -fo ES_D7_gro-seq_enhancers.fasta -name
+bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D10_gro-seq_enhancers_1kb.bed -fo ES_D10_gro-seq_enhancers.fasta -name
diff --git a/histone_centered_processing.sh b/histone_centered_processing.sh
index b197ec0..6601ca7 100644
--- a/histone_centered_processing.sh
+++ b/histone_centered_processing.sh
@@ -18,3 +18,72 @@ mv t Histone_pe_filtered_peaks.tsv
# Acutal Processing
python histone_enhancer_plots.py
+
+# Getting surround 1kb
+python extend_histone_1kb.py -e ES_D0_Histone_enhancers.bed -o ES_D0_Histone_enhancers_1kb
+python extend_histone_1kb.py -e ES_D2_Histone_enhancers.bed -o ES_D2_Histone_enhancers_1kb
+python extend_histone_1kb.py -e ES_D5_Histone_enhancers.bed -o ES_D5_Histone_enhancers_1kb
+python extend_histone_1kb.py -e ES_D7_Histone_enhancers.bed -o ES_D7_Histone_enhancers_1kb
+python extend_histone_1kb.py -e ES_D10_Histone_enhancers.bed -o ES_D10_Histone_enhancers_1kb
+
+
+# Meme processing
+#!/bin/bash
+
+#SBATCH --job-name=fasta_processing
+#SBATCH --partition=super
+#SBATCH --nodes=2
+#SBATCH --ntasks=64
+#SBATCH --time=0-36:00:00
+#SBATCH --output=fasta_processing.%j.out
+#SBATCH --error=fasta_processing.%j.err
+#SBATCH --mail-user=venkat.malladi@utsouthwestern.edu
+#SBATCH --mail-type=ALL
+# Fasta file processing
+
+module load bedtools
+bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D0_Histone_enhancers_1kb.bed -fo ES_D0_Histone_enhancers.fasta -name
+bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D2_Histone_enhancers_1kb.bed -fo ES_D2_Histone_enhancers.fasta -name
+bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D5_Histone_enhancers_1kb.bed -fo ES_D5_Histone_enhancers.fasta -name
+bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D7_Histone_enhancers_1kb.bed -fo ES_D7_Histone_enhancers.fasta -name
+bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D10_Histone_enhancers_1kb.bed -fo ES_D10_Histone_enhancers.fasta -name
+
+# Meme processing
+#!/bin/bash
+
+#SBATCH --job-name=meme_test
+#SBATCH --partition=super
+#SBATCH --nodes=2
+#SBATCH --ntasks=64
+#SBATCH --time=0-36:00:00
+#SBATCH --output=meme_test.%j.out
+#SBATCH --error=meme_test.%j.err
+#SBATCH --mail-user=venkat.malladi@utsouthwestern.edu
+#SBATCH --mail-type=ALL
+
+module load meme/4.11.0-intel-mvapich2
+
+
+#!/bin/bash
+
+#SBATCH --job-name=meme_test
+#SBATCH --output=meme_test.%j.out
+#SBATCH --error=meme_test.%j.err
+#SBATCH --mail-user=venkat.malladi@utsouthwestern.edu
+# Use super partition
+#SBATCH --partition=super
+
+# Use 2 nodes
+#SBATCH -N 2
+
+# Total of 96 tasks
+#SBATCH -n 96
+
+#SBATCH -t 1:0:0
+
+module add meme/4.11.1-gcc-openmpi
+meme-chip -meme-p -dna -meme-mod zoops -meme-nmotifs 15 -meme-minw 8 -meme-maxw 15 -meme-maxsize 20000000 -db /project/GCRB/Lee_Lab/shared/For_CBs/databases/meme_motif_databases/JASPAR/JASPAR_CORE_2016.meme ES_D0_Histone_enhancers_1kb.fasta -o MEME_op_ES_D0_Histone_enhancers_1kb_zoops
+meme -meme-p -dna -meme-mod zoops -meme-nmotifs 15 -meme-minw 8 -meme-maxw 15 -meme-maxsize 20000000 -revcomp ES_D2_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D2_H3K27ac_1kb_zoops
+meme -meme-p -dna -meme-mod zoops -meme-nmotifs 15 -meme-minw 8 -meme-maxw 15 -meme-maxsize 20000000 -revcomp ES_D5_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D5_H3K27ac_1kb_zoops
+meme -meme-p -dna -meme-mod zoops -meme-nmotifs 15 -meme-minw 8 -meme-maxw 15 -meme-maxsize 20000000 -revcomp ES_D7_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D7_H3K27ac_1kb_zoops
+meme -meme-p -dna -meme-mod zoops -meme-nmotifs 15 -meme-minw 8 -meme-maxw 15 -meme-maxsize 20000000 -revcomp ES_D10_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D10_H3K27ac_1kb_zoops
--
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