diff --git a/ES_D0_H3K27ac_filtered_peaks.bed b/ES_D0_H3K27ac_filtered_peaks.bed
new file mode 100644
index 0000000000000000000000000000000000000000..dda5d5fc00a0e5b2f69425fa7ea9d1c1850ce205
--- /dev/null
+++ b/ES_D0_H3K27ac_filtered_peaks.bed
@@ -0,0 +1,35458 @@
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diff --git a/ES_D10_H3K27ac_filtered_peaks.bed b/ES_D10_H3K27ac_filtered_peaks.bed
new file mode 100644
index 0000000000000000000000000000000000000000..6bb867cb6970d34ffc65fcf856332b6acae9fe96
--- /dev/null
+++ b/ES_D10_H3K27ac_filtered_peaks.bed
@@ -0,0 +1,31113 @@
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diff --git a/ES_D2_H3K27ac_filtered_peaks.bed b/ES_D2_H3K27ac_filtered_peaks.bed
new file mode 100644
index 0000000000000000000000000000000000000000..a193b94bbb1892543d9b6be245f0209942ac4b67
--- /dev/null
+++ b/ES_D2_H3K27ac_filtered_peaks.bed
@@ -0,0 +1,32463 @@
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diff --git a/ES_D5_H3K27ac_filtered_peaks.bed b/ES_D5_H3K27ac_filtered_peaks.bed
new file mode 100644
index 0000000000000000000000000000000000000000..6cedca1d01592ebb2e39023ca002db28f83ca994
--- /dev/null
+++ b/ES_D5_H3K27ac_filtered_peaks.bed
@@ -0,0 +1,31293 @@
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diff --git a/ES_D7_H3K27ac_filtered_peaks.bed b/ES_D7_H3K27ac_filtered_peaks.bed
new file mode 100644
index 0000000000000000000000000000000000000000..4d4c9ec119577c5ba128a44b63927a431bd5384a
--- /dev/null
+++ b/ES_D7_H3K27ac_filtered_peaks.bed
@@ -0,0 +1,32727 @@
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+chr1	53691073	53692074	H_2018
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+chrX	149444879	149445880	H_68295
+chrX	149650902	149651903	H_68299
+chrX	150134818	150135819	H_68312
+chrX	152065806	152066807	H_68322
+chrX	152126737	152127738	H_68326
+chrX	152148977	152149978	H_68327
+chrX	152647038	152648039	H_68328
+chrX	152888211	152889212	H_68332
+chrX	153084229	153085230	H_68339
+chrX	153290391	153291392	H_68350
+chrX	153311319	153312320	H_68353
+chrX	153316871	153317872	H_68354
+chrX	153357157	153358158	H_68357
+chrX	153755138	153756139	H_68364
+chrX	153962462	153963463	H_68366
+chrX	154027934	154028935	H_68368
+chrX	154146133	154147134	H_68370
+chrX	154216444	154217445	H_68372
+chrY	2649463	2650464	H_68376
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+chrY	2754498	2755499	H_68381
+chrY	2872190	2873191	H_68383
+chrY	2880350	2881351	H_68384
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+chrY	6626346	6627347	H_68393
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+chrY	6880424	6881425	H_68399
+chrY	9983521	9984522	H_68412
+chrY	10031390	10032391	H_68414
+chrY	13471995	13472996	H_68415
+chrY	13476149	13477150	H_68416
+chrY	13488385	13489386	H_68417
+chrY	14481843	14482844	H_68421
+chrY	14485577	14486578	H_68422
+chrY	14503488	14504489	H_68424
+chrY	14506873	14507874	H_68425
+chrY	14588583	14589584	H_68427
+chrY	14590558	14591559	H_68428
+chrY	14637948	14638949	H_68429
+chrY	14647943	14648944	H_68430
+chrY	14855939	14856940	H_68437
+chrY	14991137	14992138	H_68440
+chrY	15009843	15010844	H_68441
+chrY	15547196	15548197	H_68457
+chrY	15554255	15555256	H_68458
+chrY	15989863	15990864	H_68465
+chrY	16174789	16175790	H_68466
+chrY	16267719	16268720	H_68468
+chrY	16965145	16966146	H_68473
+chrY	17536071	17537072	H_68475
+chrY	17567053	17568054	H_68477
+chrY	17861146	17862147	H_68483
+chrY	18038372	18039373	H_68489
+chrY	18213575	18214576	H_68490
+chrY	21223720	21224721	H_68506
+chrY	21393694	21394695	H_68508
+chrY	21394698	21395699	H_68509
+chrY	21466223	21467224	H_68510
diff --git a/enhancers_1kb.bed b/enhancers_1kb.bed
new file mode 100644
index 0000000000000000000000000000000000000000..9a930b293f449ca0bb961cc7561989b92b15083e
--- /dev/null
+++ b/enhancers_1kb.bed
@@ -0,0 +1,68516 @@
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+chr1	1154563	1155564	H_23
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diff --git a/enhancers_renamed.bed b/enhancers_renamed.bed
new file mode 100644
index 0000000000000000000000000000000000000000..676c928b245100446ff343ff94b667d51f2f2c71
--- /dev/null
+++ b/enhancers_renamed.bed
@@ -0,0 +1,68516 @@
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+chrX	150030733	150030983	H_68307
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+chrX	150352343	150352879	H_68316
+chrX	150407671	150409257	H_68317
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+chrX	151021052	151021928	H_68320
+chrX	152062866	152063034	H_68321
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+chrY	14357897	14358145	H_68420
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+chrY	14507241	14507505	H_68425
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+chrY	14588096	14590070	H_68427
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diff --git a/histone_centered_processing.sh b/histone_centered_processing.sh
index 262a63d943ea95a9d0baba54c1ce44a09e3ca8d7..c01712ec9bd51e59d16544f656e2845b29fd1b7c 100644
--- a/histone_centered_processing.sh
+++ b/histone_centered_processing.sh
@@ -6,3 +6,38 @@ bedops --everything  H3K4me1_filtered_peaks.bed H3K27ac_filtered_peaks.bed | bed
 # Get RPKM
 ./rpkm.py --peaks Histone_putative_enhancers.bed --experiments h3k4me1_list.csv -f H3K4me1_hc
 ./rpkm.py --peaks Histone_putative_enhancers.bed --experiments h3k27ac_list.csv -f H3K27ac_hc
+
+
+# Acutal Processing
+./define_histone_window.py --enhancers H3K27ac_filtered_peaks.bed
+./rpkm_name.py --peaks enhancers_renamed.bed --experiments h3k27ac_list.csv -f H3K27ac
+
+
+# histone Processing
+bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D0_H3K27ac_filtered_peaks.bed -fo  ES_D0_H3K27ac_filtered_peaks.fasta -name
+bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D2_H3K27ac_filtered_peaks.bed -fo  ES_D2_H3K27ac_filtered_peaks.fasta -name
+bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D5_H3K27ac_filtered_peaks.bed -fo  ES_D5_H3K27ac_filtered_peaks.fasta -name
+bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D7_H3K27ac_filtered_peaks.bed -fo  ES_D7_H3K27ac_filtered_peaks.fasta -name
+bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D10_H3K27ac_filtered_peaks.bed -fo  ES_D10_H3K27ac_filtered_peaks.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
+meme -p 64 -dna -mod zoops -nmotifs 15 -minw 8 -maxw 15 -maxsize 20000000 -revcomp ES_D0_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D0_H3K27ac_1kb_zoops
+meme -p 64 -dna -mod zoops -nmotifs 15 -minw 8 -maxw 15 -maxsize 20000000 -revcomp ES_D2_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D2_H3K27ac_1kb_zoops
+meme -p 64 -dna -mod zoops -nmotifs 15 -minw 8 -maxw 15 -maxsize 20000000 -revcomp ES_D5_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D5_H3K27ac_1kb_zoops
+meme -p 64 -dna -mod zoops -nmotifs 15 -minw 8 -maxw 15 -maxsize 20000000 -revcomp ES_D7_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D7_H3K27ac_1kb_zoops
+meme -p 64 -dna -mod zoops -nmotifs 15 -minw 8 -maxw 15 -maxsize 20000000 -revcomp ES_D10_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D10_H3K27ac_1kb_zoops
diff --git a/rpkm_name.py b/rpkm_name.py
new file mode 100755
index 0000000000000000000000000000000000000000..9363f108584c9986cebdd692f5456c63da384b5b
--- /dev/null
+++ b/rpkm_name.py
@@ -0,0 +1,93 @@
+#!/usr/bin/env python
+
+# -*- coding: latin-1 -*-
+'''Take an BED file and list of Alignments and caluclates RPKM for a minimum score'''
+
+EPILOG = '''
+For more details:
+        %(prog)s --help
+'''
+
+import numpy
+import pybedtools
+from pybedtools.featurefuncs import normalized_to_length
+import pysam
+import pandas as pd
+import argparse
+import csv
+import math
+import os
+from sklearn import preprocessing
+
+
+def get_args():
+    parser = argparse.ArgumentParser(
+            description=__doc__, epilog=EPILOG,
+            formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+    parser.add_argument('-p', '--peaks',
+    	help="The peak file used to calculate RPKM.",
+        required = True)
+    parser.add_argument('-c', '--centered',
+    	help="The peak 1kb file.",
+        required = True)
+    parser.add_argument('-e','--experiments',
+    	help="Comma seperate file of experiment name followd by file location.",
+        required = True)
+    parser.add_argument('-f','--factor',
+    	help="Factor that is being analyzed.",
+        required = True)
+    parser.add_argument('--minimum',
+    	default = 1,
+        type=int,
+    	help="The minimum RPKM value that at least 1 of experiements has to have per genomic location. Default is --minimum=1")
+    args = parser.parse_args()
+    return args
+
+
+def rpkm(peak_file,aln_file,exp_name,columns):
+    ''' Return Pandas Dataframe of RPKM value and location'''
+    columns.append(exp_name)
+    ## RPKM  =   numReads / (geneLength/1000 * totalNumReads/1,000,000 )
+    peak_counts = peak_file.multi_bam_coverage(bams=[aln_file])
+    total_counts = reduce(lambda x, y: x + y, [ int(l.rstrip('\n').split('\t')[2]) for l in pysam.idxstats(aln_file)])
+    rpkm = peak_counts.each(normalized_to_length, 4, float(math.pow(10,9))/total_counts).saveas("test.bed")
+    rpkm_df = rpkm.to_dataframe()
+    #os.remove('test.bed')
+    rpkm_df.columns = columns
+    columns.remove(exp_name)
+    return rpkm_df
+
+
+def main():
+    args = get_args()
+    peak_file = pybedtools.BedTool(args.peaks)
+    centered_file = pybedtools.BedTool(args.centered)
+    experiment_dict = csv.DictReader(open(args.experiments))
+
+    # Create dataframe from peak file
+    for exp in experiment_dict:
+        rpkm_columns = []
+        peak_df = peak_file.to_dataframe()
+        centered_df = centered_file.to_dataframe()
+        columns = list(peak_df.columns.values)
+        experiment = exp['experiment']
+        aln_file = exp['file']
+        rpkm_columns.append(experiment)
+        peak_df = pd.merge(peak_df,rpkm(peak_file,aln_file,experiment,columns))
+
+
+        # Filter for alteast Min RPKM in experiment condition
+        peak_rpkm_only = peak_df[rpkm_columns]
+        scaler = preprocessing.StandardScaler(with_mean=False)
+        norm = scaler.fit_transform(peak_rpkm_only.values)
+        peak_rpkm_std_robust = pd.DataFrame(data=norm, columns=list(peak_rpkm_only.columns.values), index = peak_rpkm_only.index )
+        filtered_rpkm = centered_df[peak_df[experiment] >= args.minimum]
+
+        # Write out RPKM matrix
+        filtered_peaks = filtered_rpkm[columns]
+        pybedtools.BedTool.from_dataframe(filtered_peaks).saveas(experiment + '_' + args.factor + '_filtered_peaks.bed')
+
+
+if __name__ == '__main__':
+    main()