.gitmodules

 [submodule "MakeGencodeTSS"]
 	path = MakeGencodeTSS
 	url = https://github.com/sdjebali/MakeGencodeTSS
+[submodule "dREG"]
+	path = dREG
+	url = https://github.com/Danko-Lab/dREG
+[submodule "bigWig"]
+	path = bigWig
+	url = https://github.com/andrelmartins/bigWig.git
+[submodule "dREG-Model"]
+	path = dREG-Model
+	url = https://github.com/Danko-Lab/dREG-Model

README.md

+# Total Functional Score of Enhancer Elements Identifies Lineage-Specific Enhancers that Drive Differentiation of Pancreatic Cells
 
+This directory contains the scripts for identification of TFs maintaining multipotency of endodermal stem cells during differentiation into pancreatic lineages
+,using TFSEE.
 
-Random Forest of Enhancer Prediction
-http://enhancer.ucsd.edu/renlab/RFECS_enhancer_prediction/
 
+## Dependencies for TFSEE
 
+This code requires python 2.7+ to run.
 
+The pythons scripts require the following python packages:
+- biopython-1.70
+- pandas-0.20.1
+- numpy-1.12.1
+- scikit-learn-0.18.1
+- matplotlib-2.0.2
+- seaborn-0.8.1
+- scipy-0.19.0
 
-# Methods:
 
-1. Call Peaks H3K27ac, H3K4me1 using threshold of 1e-2
-2. Call Peaks H3K4me3 using threshold of 1e-5
-3. Call Transcript units per cell using GRO-seq and GRO-HMM
-4. Merge H3K27ac, H3K4me1, H3K4me3 Peaks within 500bp and make universe filter for at least 1 RPKM in a cell
-5. Merge GRO-seq transcripts and filter for
-    a. +/- 3kb from TSS of protein coding genes Gencode and H3K4me3 pekas
-    b. Merge overlaping transcripts
-    c. Filter for <=9kb Short-Short-Paired and Short-Unpaired
-    d. make universe filter for at least 1 > RPKM SSP and > 2 RPM SUP in a cell
-6. Make Enhancer regions for motif search
-    a. Short-Short-Paired +/- 500 bp center-overlap
-    b. Short-Unpaired +/- bp TSS of transcript
-    c. Histone data +/- bp 500 bp center of mark
-7. De novo motif analyses were performed using the command-line version of MEME (Bailey et al., 2009). The
-following parameters were used for motif prediction: (1) zero or one occurrence per sequence (-
-mod zoops); (2) number of motifs (-nmotifs 15); (3) minimum, maximum width of the motif (-
-minw 8, -maxw 15); and (4) search for motif in given strand and reverse complement strand (-
-revcomp). The predicted motifs from MEME were matched to known motifs using TOMTOM
-(Gupta et al., 2007).
+Install the dependencies.
+
+```sh
+pip install -r requirements.txt
+```
+
+
+#### Pipeline Description
+
+##### Pre-processing Steps
+
+1. De novo identification of enhancers using GRO-seq and [groHMM](http://www.bioconductor.org/packages/release/bioc/html/groHMM.html)
+or ChIP-seq (H3K4me1 and H3K27ac)
+
+2. Normalize Enhancer Expression using GRO-seq: For each cell line, quantify the GRO-seq reads, RPKM, that fall within a 1 kb region around the center of the overlap for paired enhancer transcripts or from the 5′ end of unpaired enhancer transcripts
+
+3. Normalize Enhancer Expression using ChIP-seq: For each cell line, quantify the ChIP-seq reads, RPKM, from H3K4me1, H3K27ac, and input for each enhancer within the universe of GRO-seq-defined enhancers
+
+4. Motif Predictions: De novo motif analyses on a 1 kb region of expressed enhancers for each cell line using [MEME](http://meme-suite.org/) and  matched to known motifs using TOMTOM and  [JASPAR](http://jaspar.genereg.net/)
+
+5. Normalize Transcription Factor Expression using RNA-seq:  For each cell line, quantify the RNA-seq reads, FPKM, for each  transcription factor that is a binding target for the motifs
+* RNA-seq analysis: RNA-seq_star.sh
+* FPKM processing RNA-seq: rnaseq_processing.sh
+
+6. Calculate TFSEE score to determining cell-type specific enhancer activity, generating:
+* unsupervised hierarchical clustering
+* tSNE representation
+* boxplot representations
+* rank order TF plots
+
+#### Data Source
+
+All dta available from NCBI’s Gene Expression Omnibus [@url:https://www.ncbi.nlm.nih.gov/geo/] or EMBL-EBI’s ArrayExpress [@url:http://www.ebi.ac.uk/arrayexpress/] repositories using the accession numbers listed:
+
+| Assay | Accessions |
+| :--------------------: | :------------------------------------------------------------: |
+| GRO-seq | GSM1316306, GSM1316313, GSM1316320, GSM1316327, GSM1316334 |
+| H3K4me3 ChIP-seq | ERR208008, ERR208014, ERR207998, ERR20798, ERR207999 |
+| H3K4me1 ChIP-seq | GSM1316302, GSM1316303, GSM1316309, GSM1316316, GSM1316317, GSM1316310, GSM1316323, GSM1316324, GSM1316330, GSM1316331 |
+| H3K27ac ChIP-seq | GSM1316300, GSM1316301, GSM1316307, GSM1316308, GSM1316314, GSM1316315, GSM1316321, GSM1316322, GSM1316328, GSM1316329 |
+| Input ChIP-seq | ERR208001, ERR208012, ERR207984, ERR208011, ERR207986, GSM1316304, GSM1316305, GSM1316311, GSM1316312, GSM1316318, GSM1316319, GSM1316325, GSM1316326, GSM1316332, GSM1316333 |
+| RNA-seq | ERR266333, ERR266335, ERR266337, ERR266338, ERR266341, ERR266342, ERR266344, ERR266346, ERR266349, ERR266351 |
+
+
+### Main Scripts
+
+- Compute TFSEE to identify cognate transcription factors are under 'analysis'
+ * Applicable to either enhancer method:
+    * Get H3K4me3 peaks: h3k4me3_processing.sh
+    * Get H3K27ac peaks: h3k27ac_processing.sh
+    * Get H3K4me1 peaks: h3k4me1_processing.sh
+    * Exclude regions based on H3K4me3 and promoters: excluded_regions_processing.sh
+    * RNA-seq analysis: RNA-seq_star.sh
+    * FPKM processing RNA-seq: rnaseq_processing.sh
+ * TFSEE using GRO-seq:
+      * Tune GroHMM: tune-hmm.sh
+      * Call Transcripts: call-transcripts.sh
+      * Make universe of Enhancers: groseq_processing.sh
+      * GRO_seq_TFSEE:
+         * TFSEE pre-processing: tfsee_processing.sh
+         * TFSEE score integration: matrix_analysis.py
+         * Rank order TF's clusters: rank_order.py
+ * TFSEE using histone modifications ChIP-seq:
+      * Make universe of Enhancers: histone_centered_processing.sh
+      * Histone_TFSEE:
+         * TFSEE pre-processing: tfsee_processing.sh
+         * TFSEE score integration: matrix_analysis.py
+         * Rank order TF's clusters: rank_order.py

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-chr4	97066099	97071199	SSP_23038	0	+
-chr4	97069549	97073649	SSP_23038	0	-
-chr4	111938199	111941049	SSP_23232	0	+
-chr4	111940799	111940949	SSP_23232	0	-
-chr4	125179499	125182949	SSP_23465	0	+
-chr4	125179499	125182949	SSP_23464	0	+
-chr4	125180999	125181149	SSP_23464	0	-
-chr4	125182199	125184299	SSP_23465	0	-
-chr4	134211749	134211899	SSP_23723	0	+
-chr4	134211749	134211899	SSP_23723	0	-
-chr4	134226649	134228199	SSP_23724	0	+
-chr4	134227549	134227999	SSP_23724	0	-
-chr4	134239949	134248949	SSP_23725	0	-
-chr4	134243049	134243299	SSP_23725	0	+
-chr4	134265699	134271599	SSP_23726	0	-
-chr4	134265749	134265899	SSP_23726	0	+
-chr4	134283799	134291449	SSP_23727	0	-
-chr4	134287649	134290499	SSP_23727	0	+
-chr4	134318149	134319099	SSP_23728	0	+
-chr4	134318449	134318599	SSP_23728	0	-
-chr4	134361649	134367399	SSP_23731	0	+
-chr4	134362299	134365699	SSP_23731	0	-
-chr4	134374549	134377999	SSP_23732	0	-
-chr4	134374549	134377999	SSP_23733	0	-
-chr4	134374749	134374899	SSP_23732	0	+
-chr4	134377799	134383799	SSP_23733	0	+
-chr4	134377799	134383799	SSP_23734	0	+
-chr4	134382149	134382399	SSP_23734	0	-
-chr4	136908899	136916999	SSP_23827	0	+
-chr4	136914249	136918399	SSP_23827	0	-
-chr4	136914249	136918399	SSP_23829	0	-
-chr4	136917699	136917849	SSP_23829	0	+
-chr4	165656549	165664399	SSP_24333	0	+
-chr4	165656649	165663249	SSP_24333	0	-
-chr4	179493199	179502099	SSP_24588	0	+
-chr4	179501949	179502299	SSP_24588	0	-
-chr5	18953599	18956699	SSP_25228	0	+
-chr5	18953849	18954299	SSP_25228	0	-
-chr5	26590999	26593449	SSP_25415	0	+
-chr5	26591049	26591499	SSP_25415	0	-
-chr5	28617049	28623099	SSP_25535	0	-
-chr5	28617149	28623249	SSP_25535	0	+
-chr5	34600599	34606999	SSP_25708	0	+
-chr5	34601299	34608349	SSP_25708	0	-
-chr5	34601299	34608349	SSP_25710	0	-
-chr5	34608149	34616549	SSP_25710	0	+
-chr5	57318899	57324099	SSP_26088	0	+
-chr5	57318949	57324099	SSP_26088	0	-
-chr5	66597049	66599599	SSP_26223	0	+
-chr5	66597099	66601149	SSP_26223	0	-
-chr5	66597099	66601149	SSP_26224	0	-
-chr5	66600999	66601149	SSP_26224	0	+
-chr5	71711549	71718949	SSP_26277	0	+
-chr5	71711549	71718949	SSP_26278	0	+
-chr5	71711549	71711699	SSP_26277	0	-
-chr5	71714499	71720599	SSP_26278	0	-
-chr5	84382799	84389599	SSP_26371	0	-
-chr5	84382899	84383149	SSP_26371	0	+
-chr5	86197899	86200049	SSP_26463	0	+
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-chr5	119768849	119774699	SSP_26980	0	+
-chr5	119773349	119774349	SSP_26980	0	-
-chr5	143352799	143355299	SSP_27234	0	+
-chr5	143352799	143355299	SSP_27235	0	+
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-chr5	143354999	143355149	SSP_27235	0	-
-chr5	146474499	146479199	SSP_27268	0	+
-chr5	146474799	146480149	SSP_27268	0	-
-chr5	146492349	146494649	SSP_27269	0	-
-chr5	146493199	146494749	SSP_27269	0	+
-chr5	161691149	161692349	SSP_27413	0	+
-chr5	161692049	161697299	SSP_27413	0	-
-chr5	174537199	174543149	SSP_27574	0	+
-chr5	174537199	174542399	SSP_27574	0	-
-chr6	18833499	18841599	SSP_27799	0	-
-chr6	18833749	18836749	SSP_27799	0	+
-chr6	18936499	18942799	SSP_27806	0	+
-chr6	18937799	18942749	SSP_27806	0	-
-chr6	58146799	58154349	SSP_28325	0	+
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-chr6	58706899	58707249	SSP_28348	0	+
-chr6	63518249	63519299	SSP_28384	0	-
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-chr6	63604199	63609249	SSP_28385	0	+
-chr6	63606849	63607249	SSP_28385	0	-
-chr6	85389649	85397749	SSP_28731	0	-
-chr6	85390049	85394099	SSP_28731	0	+
-chr6	87304749	87312049	SSP_28769	0	-
-chr6	87306099	87310699	SSP_28769	0	+
-chr6	113371399	113375449	SSP_29229	0	+
-chr6	113372049	113372199	SSP_29229	0	-
-chr6	122531749	122534099	SSP_29394	0	+
-chr6	122532799	122535449	SSP_29394	0	-
-chr6	133341799	133341999	SSP_29482	0	-
-chr6	133341849	133347649	SSP_29482	0	+
-chr6	137735049	137736749	SSP_29529	0	+
-chr6	137736449	137736949	SSP_29529	0	-
-chr6	142966699	142973149	SSP_29661	0	-
-chr6	142969399	142973249	SSP_29661	0	+
-chr7	8953399	8958999	SSP_30052	0	+
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-chr7	9242799	9244449	SSP_30066	0	-
-chr7	9242899	9246749	SSP_30066	0	+
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-chr7	80962899	80965199	SSP_30926	0	-
-chr7	80965949	80966099	SSP_30927	0	-
-chr7	89043149	89050799	SSP_31097	0	-
-chr7	89043449	89047549	SSP_31097	0	+
-chr7	115032699	115036999	SSP_31310	0	+
-chr7	115032699	115037249	SSP_31310	0	-
-chr7	118158999	118162899	SSP_31382	0	+
-chr7	118158999	118162899	SSP_31383	0	+
-chr7	118159649	118160449	SSP_31382	0	-
-chr7	118162399	118169199	SSP_31383	0	-
-chr7	118339799	118344199	SSP_31393	0	+
-chr7	118340049	118344149	SSP_31393	0	-
-chr7	137926649	137930649	SSP_31617	0	-
-chr7	137927049	137934449	SSP_31617	0	+
-chr7	155962149	155967449	SSP_31738	0	-
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-chr8	305549	310899	SSP_31761	0	-
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-chr8	4886499	4892699	SSP_31803	0	+
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-chr8	55107549	55112999	SSP_32430	0	-
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-chr8	92448349	92455749	SSP_33017	0	-
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-chr8	116227749	116227899	SSP_33309	0	+
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-chr9	12319449	12322299	SSP_33982	0	-
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-chr9	20048949	20055899	SSP_34108	0	-
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-chr9	30225499	30229049	SSP_34366	0	-
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-chrX	38832049	38836049	SSP_35880	0	-
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-chrY	3547249	3555799	SSP_37802	0	+
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-chrY	26838249	26841549	SSP_38380	0	-
-chrY	26841149	26841699	SSP_38380	0	+

SSP_filtered_peaks_merged.bed

-chr14	84597499	84602349	SSP_10334
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-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

SUNP_filtered_peaks.bed

-chr1	28859449	28861399	SUNP_973	0	-
-chr1	31967499	31970649	SUNP_1116	0	-
-chr1	38077299	38078299	SUNP_1296	0	+
-chr1	51131749	51131899	SUNP_1817	0	+
-chr1	110998199	111004299	SUNP_5265	0	-
-chr1	210543499	210547699	SUNP_9034	0	-
-chr1	213731799	213739949	SUNP_9160	0	-
-chr1	223183699	223189299	SUNP_9841	0	-
-chr1	223196599	223196749	SUNP_9842	0	-
-chr1	223202649	223203699	SUNP_9843	0	-
-chr10	9206299	9206449	SUNP_11595	0	+
-chr10	24983949	24984099	SUNP_12409	0	+
-chr10	53361449	53362349	SUNP_13655	0	-
-chr10	63892949	63896749	SUNP_14421	0	+
-chr10	106439849	106444899	SUNP_16437	0	-
-chr11	12741449	12746299	SUNP_18699	0	-
-chr11	14133299	14136599	SUNP_18780	0	-
-chr11	27633949	27634099	SUNP_19656	0	-
-chr11	27645299	27654149	SUNP_19658	0	-
-chr11	79831349	79831499	SUNP_21858	0	+
-chr11	85194799	85202099	SUNP_22249	0	+
-chr11	92976499	92980299	SUNP_22750	0	+
-chr11	132844299	132845999	SUNP_25038	0	+
-chr12	41777749	41782199	SUNP_27215	0	-
-chr12	85559149	85562849	SUNP_29439	0	-
-chr12	102909899	102910049	SUNP_30435	0	-
-chr12	112702699	112706599	SUNP_30825	0	+
-chr13	23275549	23275899	SUNP_31955	0	-
-chr13	27614499	27617999	SUNP_32172	0	+
-chr13	54689149	54689299	SUNP_33694	0	-
-chr13	54814199	54814349	SUNP_33704	0	-
-chr13	54815749	54815899	SUNP_33705	0	-
-chr13	102853149	102861449	SUNP_37011	0	+
-chr13	110072799	110079049	SUNP_37534	0	-
-chr14	68922149	68927049	SUNP_40401	0	-
-chr14	85737649	85738399	SUNP_41232	0	+
-chr14	99435449	99439699	SUNP_42068	0	-
-chr14	107090849	107092849	SUNP_42359	0	+
-chr15	49567049	49571249	SUNP_43859	0	-
-chr15	84760549	84761149	SUNP_45370	0	-
-chr17	75154849	75158449	SUNP_52076	0	-
-chr18	8639149	8641099	SUNP_52797	0	-
-chr18	10439049	10439199	SUNP_52891	0	+
-chr2	44672749	44676149	SUNP_60562	0	-
-chr2	50625349	50627099	SUNP_60899	0	+
-chr2	78922999	78930799	SUNP_62456	0	+
-chr2	81722749	81727049	SUNP_62699	0	-
-chr2	88206349	88207049	SUNP_63049	0	+
-chr2	108458799	108462499	SUNP_63983	0	-
-chr2	117769699	117770149	SUNP_64454	0	+
-chr2	122598249	122598399	SUNP_64716	0	-
-chr2	159438099	159441249	SUNP_67051	0	-
-chr2	161816599	161819799	SUNP_67168	0	+
-chr2	187050599	187056349	SUNP_68696	0	+
-chr2	234095249	234095899	SUNP_71221	0	-
-chr2	238247249	238252299	SUNP_71541	0	+
-chr20	11055849	11056399	SUNP_72429	0	+
-chr21	17586899	17592749	SUNP_75253	0	-
-chr21	18824899	18829499	SUNP_75333	0	-
-chr21	25735899	25739549	SUNP_75806	0	+
-chr21	27226849	27228449	SUNP_75909	0	+
-chr21	39590049	39595299	SUNP_76496	0	-
-chr3	14477749	14479649	SUNP_79000	0	-
-chr3	32157249	32157399	SUNP_80136	0	-
-chr3	37569249	37573899	SUNP_80419	0	-
-chr3	54658599	54665349	SUNP_81081	0	-
-chr3	85367249	85370499	SUNP_83009	0	-
-chr3	134502099	134507199	SUNP_85761	0	-
-chr3	134678749	134678949	SUNP_85774	0	-
-chr3	158111699	158117049	SUNP_87010	0	-
-chr3	174600799	174605499	SUNP_88066	0	-
-chr3	177311449	177312099	SUNP_88254	0	-
-chr3	196316299	196316449	SUNP_89235	0	-
-chr4	9397799	9398799	SUNP_89700	0	+
-chr4	47438499	47447299	SUNP_92182	0	+
-chr4	49275549	49277899	SUNP_92251	0	+
-chr4	69165399	69169499	SUNP_93198	0	+
-chr4	89598149	89606799	SUNP_94284	0	-
-chr4	102761049	102765049	SUNP_95202	0	-
-chr4	131346099	131349349	SUNP_96870	0	+
-chr4	143613799	143615649	SUNP_97623	0	+
-chr4	167524849	167524999	SUNP_99095	0	+
-chr5	3508849	3512799	SUNP_100697	0	+
-chr5	94824399	94828499	SUNP_106129	0	+
-chr5	136628099	136629549	SUNP_108767	0	+
-chr5	146440099	146440249	SUNP_109152	0	+
-chr5	156284099	156288199	SUNP_109686	0	-
-chr5	158592499	158592849	SUNP_109802	0	+
-chr6	4425299	4431999	SUNP_111239	0	+
-chr6	23940549	23944049	SUNP_112350	0	+
-chr6	25658199	25658649	SUNP_112441	0	-
-chr6	26779299	26781249	SUNP_112472	0	+
-chr6	53082199	53084249	SUNP_113514	0	+
-chr6	106779699	106786049	SUNP_116729	0	+
-chr6	133371449	133371649	SUNP_118187	0	-
-chr6	147693499	147695149	SUNP_119052	0	-
-chr6	160515099	160522199	SUNP_119708	0	-
-chr6	165822349	165824699	SUNP_120052	0	+
-chr7	53431449	53433999	SUNP_123409	0	+
-chr7	145691949	145694599	SUNP_127964	0	+
-chr8	4377249	4379899	SUNP_129007	0	+
-chr8	34313649	34315699	SUNP_130571	0	-
-chr8	36088549	36089649	SUNP_130682	0	-
-chr8	59426999	59432849	SUNP_131857	0	+
-chr9	75669699	75669849	SUNP_140288	0	+
-chr9	76717349	76720199	SUNP_140368	0	+
-chr9	110018249	110018899	SUNP_142250	0	-
-chrX	11678399	11678799	SUNP_144215	0	+
-chrX	13683449	13687849	SUNP_144336	0	-
-chrX	24820949	24824299	SUNP_144816	0	-
-chrX	102676249	102679449	SUNP_148801	0	-
-chrX	122184999	122185949	SUNP_149759	0	+
-chrX	150872299	150873799	SUNP_151471	0	-
-chrY	5501699	5508249	SUNP_151888	0	-

SUNP_filtered_peaks.tsv

-chrom	start	end	name	score	strand	ES_D0	ES_D2	ES_D5	ES_D7	ES_D10
-chr1	28859449	28861399	SUNP_973	0	-	12.754866991	9.27189492446	0.0482292018793	0.14916782477	34.3642475304
-chr1	31967499	31970649	SUNP_1116	0	-	0.0591450939481	0.111549804324	11.3453455849	5.54051920573	0.0264590865847
-chr1	38077299	38078299	SUNP_1296	0	+	6.90769201088	4.00894785404	11.3326567116	8.01990155029	9.50145799255
-chr1	51131749	51131899	SUNP_1817	0	+	2.38855187098	12.4580849648	0.313489812215	1.10810384115	1.66692245483
-chr1	110998199	111004299	SUNP_5265	0	-	28.9234053282	21.1038597764	0.0	0.0272484551101	10.7735111118
-chr1	210543499	210547699	SUNP_9034	0	-	16.2694504583	8.69327906881	12.4276318414	1.90950036912	2.18287464323
-chr1	213731799	213739949	SUNP_9160	0	-	14.2653696098	11.3625887409	0.0288487557253	0.0866768342001	9.0249022478
-chr1	223183699	223189299	SUNP_9841	0	-	13.0555686105	5.62724396416	0.0251911456244	0.00742033822196	0.0
-chr1	223196599	223196749	SUNP_9842	0	-	16.051068573	3.83325691223	0.313489812215	0.0	0.0
-chr1	223202649	223203699	SUNP_9843	0	-	7.20660221645	12.9752704212	0.0	0.0	0.039688629877
-chr10	9206299	9206449	SUNP_11595	0	+	2.4363229084	2.98142204285	99.3762704722	0.0	0.0
-chr10	24983949	24984099	SUNP_12409	0	+	20.3982329782	17.4626148224	10.3451638031	2.21620768229	5.27858777364
-chr10	53361449	53362349	SUNP_13655	0	-	7.74686990155	14.4102065404	0.261241510179	4.57092834473	3.65796872033
-chr10	63892949	63896749	SUNP_14421	0	+	13.9843426383	12.7733199082	1.96756105825	0.0874818821957	1.46952374308
-chr10	106439849	106444899	SUNP_16437	0	-	25.9751468615	22.3258750358	0.42833261471	0.510166619933	6.78321909838
-chr11	12741449	12746299	SUNP_18699	0	-	5.18882113663	5.25590896213	8.38666044019	46.2918947452	0.833461227417
-chr11	14133299	14136599	SUNP_18780	0	-	22.8236988326	20.6376356992	0.0	0.0503683564157	19.9525566563
-chr11	27633949	27634099	SUNP_19656	0	-	26.1307574685	0.851834869385	0.0	0.0	0.0
-chr11	27645299	27654149	SUNP_19658	0	-	33.6526716656	0.611805128647	0.0106267732954	0.0140860657773	0.00470882049388
-chr11	79831349	79831499	SUNP_21858	0	+	5.73252449036	6.06932344437	1.25395924886	26.0404402669	1.11128163656
-chr11	85194799	85202099	SUNP_22249	0	+	1669.44266554	1554.79919706	1712.99422156	1901.25572958	1967.77912338
-chr11	92976499	92980299	SUNP_22750	0	+	30.014668524	22.2093525485	0.0247491957012	0.0874818821957	16.9982224013
-chr11	132844299	132845999	SUNP_25038	0	+	70.7418812659	54.2574967356	1.05111289978	5.35311929142	40.5209237918
-chr12	41777749	41782199	SUNP_27215	0	-	11.3169050894	10.0676831824	0.0211341446437	0.0560277223051	14.2437587292
-chr12	85559149	85562849	SUNP_29439	0	-	16.9361238744	8.96153305157	87.3238580972	15.8803259937	0.0
-chr12	102909899	102910049	SUNP_30435	0	-	26.2740705808	31.4114108086	6.58328605652	8.31077880859	2.22256327311
-chr12	112702699	112706599	SUNP_30825	0	+	3.06285843764	4.45984698442	18.5923573245	34.1061576491	18.9024732218
-chr13	23275549	23275899	SUNP_31955	0	-	198.918599815	153.604080554	0.403058329991	0.356176234654	183.004272363
-chr13	27614499	27617999	SUNP_32172	0	+	22.0640772973	19.5450468513	0.188093887329	0.273068446568	18.5980919604
-chr13	54689149	54689299	SUNP_33694	0	-	0.191084149679	17.9950116158	0.313489812215	0.0	0.0
-chr13	54814199	54814349	SUNP_33704	0	-	24.8409394582	30.1336585045	0.0	0.277025960286	0.0
-chr13	54815749	54815899	SUNP_33705	0	-	11.4172779433	14.8006308556	0.0	0.0	0.0
-chr13	102853149	102861449	SUNP_37011	0	+	4.90199910486	5.79414486081	2.24352949947	333.567626313	0.261084239914
-chr13	110072799	110079049	SUNP_37534	0	-	62.336617813	34.2284287216	125.895000667	100.4208025	90.3872031909
-chr14	68922149	68927049	SUNP_40401	0	-	16.8217421461	14.9907725675	0.259108926423	0.101764638473	14.7896844335
-chr14	85737649	85738399	SUNP_41232	0	+	0.840770258586	0.447213306427	18.7466907705	0.387836344401	45.9514956716
-chr14	99435449	99439699	SUNP_42068	0	-	3.07027267557	2.86366839914	12.7239982605	3.65674267578	3.3926774669
-chr14	107090849	107092849	SUNP_42359	0	+	125.578114617	97.3567396188	431.205236702	2990.75841595	59.6341508217
-chr15	49567049	49571249	SUNP_43859	0	-	1.59179921116	3.24381760529	0.0	0.0593627057757	14.9030805188
-chr15	84760549	84761149	SUNP_45370	0	-	9.78111991167	9.26370420456	35.6594661395	2.49323364258	1.87528776169
-chr17	75154849	75158449	SUNP_52076	0	-	222.121390782	158.441285706	193.070538098	148.659055939	336.949852884
-chr18	8639149	8641099	SUNP_52797	0	-	2.14234729351	2.08863357397	0.65109422537	0.277025960286	12.0317607958
-chr18	10439049	10439199	SUNP_52891	0	+	49.7774209913	79.2206428528	1182.17008186	79.5064506022	45.5625470988
-chr2	44672749	44676149	SUNP_60562	0	-	3.9895841398	8.12688046343	2.04690406799	808.504339007	4.47372570599
-chr2	50625349	50627099	SUNP_60899	0	+	188.206968339	147.799434373	3.38568997192	1566.3443546	0.0714395337786
-chr2	78922999	78930799	SUNP_62456	0	+	30.6607379592	31.1697845716	18.1341799066	26.0830596454	21.0288678918
-chr2	81722749	81727049	SUNP_62699	0	-	0.266629046063	0.282294113691	23.2930220937	20.7382922363	0.222902421286
-chr2	88206349	88207049	SUNP_63049	0	+	73.0385039977	299.06249017	0.873293048314	18.3430760847	0.65486239297
-chr2	108458799	108462499	SUNP_63983	0	-	1.37503121221	2.56845480043	0.0254180928823	0.0561539108689	17.5364747444
-chr2	117769699	117770149	SUNP_64454	0	+	136.322617117	149.355047099	274.303585688	561.25459554	673.436671753
-chr2	122598249	122598399	SUNP_64716	0	-	52.3092859745	50.2582572937	105.646066717	26.8715181478	0.833461227417
-chr2	159438099	159441249	SUNP_67051	0	-	216.653028755	146.784331154	111.900934875	117.274323188	4.90816056146
-chr2	161816599	161819799	SUNP_67168	0	+	28.7096470667	24.2623201177	1.64582151413	0.597337226868	1.43251148462
-chr2	187050599	187056349	SUNP_68696	0	+	21.121860345	16.8246645778	0.547925671785	0.238483217986	0.00724748893406
-chr2	234095249	234095899	SUNP_71221	0	-	236.124888575	174.462333826	0.144687605638	0.127858135517	93.4117698728
-chr2	238247249	238252299	SUNP_71541	0	+	56.9988883113	41.242302092	0.0465578929032	0.0575994570893	12.4193974976
-chr20	11055849	11056399	SUNP_72429	0	+	51.50152116	44.1114943158	0.427486107566	0.982182950107	122.291492823
-chr21	17586899	17592749	SUNP_75253	0	-	14.458700659	14.8688868547	0.040191001566	0.255716271034	11.2125467688
-chr21	18824899	18829499	SUNP_75333	0	-	14.6226107041	11.0935288357	10.355386297	7.30806527843	0.824401866249
-chr21	25735899	25739549	SUNP_75806	0	+	8.23166958495	11.1015671077	0.876053721807	0.352923483653	0.730705733626
-chr21	27226849	27228449	SUNP_75909	0	+	169.933522861	138.576230353	121.496895347	229.819005241	483.459603229
-chr21	39590049	39595299	SUNP_76496	0	-	17.18528949	13.0148198972	0.00895685177758	0.063320219494	12.3669770697
-chr3	14477749	14479649	SUNP_79000	0	-	30.9594036456	22.7473535186	1.95518646039	2.16517658434	38.9094794063
-chr3	32157249	32157399	SUNP_80136	0	-	21.1147985395	22.2541859627	0.0	1.38512980143	8.05679186503
-chr3	37569249	37573899	SUNP_80419	0	-	15.2189279212	11.9188185353	0.0101125745876	0.0357452851983	13.8641346109
-chr3	54658599	54665349	SUNP_81081	0	-	31.1955490136	2.16981270896	0.0	0.00615613245081	0.0
-chr3	85367249	85370499	SUNP_83009	0	-	10.9667603135	12.2221922317	0.332781492967	0.23014464393	19.5542826432
-chr3	134502099	134507199	SUNP_85761	0	-	37.4061273301	31.442728267	18.624982961	14.5357150927	10.1567873106
-chr3	134678749	134678949	SUNP_85774	0	-	6.34160521746	6.5484805584	3.52676038742	30.957651062	8.12624696732
-chr3	158111699	158117049	SUNP_87010	0	-	0.237069353924	0.286598647643	0.0	0.0233012489961	11.8086656146
-chr3	174600799	174605499	SUNP_88066	0	-	35.1711721989	27.424098654	0.0300149820206	0.0442062702585	4.2205057899
-chr3	177311449	177312099	SUNP_88254	0	-	18.4543192247	15.5787492459	0.65109422537	0.767148813101	0.64112402109
-chr3	196316299	196316449	SUNP_89235	0	-	15.477816124	31.9438076019	17.555429484	2.21620768229	3.05602450053
-chr4	9397799	9398799	SUNP_89700	0	+	36.1220699449	47.2448914433	3.62080733109	1.53749407959	2.91711429596
-chr4	47438499	47447299	SUNP_92182	0	+	13.863915053	12.5923941558	0.363363191431	0.0519423675537	0.0662980521809
-chr4	49275549	49277899	SUNP_92251	0	+	20.6157436592	34.0983154764	5.66282660789	1.538378205	0.265998264069
-chr4	69165399	69169499	SUNP_93198	0	+	11.534957816	49.4310944708	1.36482759708	1.55066970453	0.0914774517897
-chr4	89598149	89606799	SUNP_94284	0	-	3.73276811467	4.32626249776	15.4171752736	16.2324402279	9.57757757286
-chr4	102761049	102765049	SUNP_95202	0	-	1.30594073546	2.66730793476	0.0587793397903	0.0311654205322	16.1378930159
-chr4	131346099	131349349	SUNP_96870	0	+	6.7599692644	59.4203965715	0.549812901424	0.0255716271034	17.4513958541
-chr4	143613799	143615649	SUNP_97623	0	+	29.4682745423	27.6357103064	0.864215157999	2.06646391997	0.292837728552
-chr4	167524849	167524999	SUNP_99095	0	+	708.540027008	552.414912796	4.0753675588	4.70944132487	455.625470988
-chr5	3508849	3512799	SUNP_100697	0	+	64.2550688128	48.9023302706	1.90474822612	2.01983484968	18.3783475717
-chr5	94824399	94828499	SUNP_106129	0	+	14.8119344682	25.9913517463	0.596395252507	0.010135096108	20.9381722985
-chr5	136628099	136629549	SUNP_108767	0	+	4.95665695158	6.24556514148	12.2909626375	10.3454867238	0.287400423247
-chr5	146440099	146440249	SUNP_109152	0	+	0.0477710374196	12.2451262474	0.62697962443	0.0	0.0
-chr5	156284099	156288199	SUNP_109686	0	-	12.5224201138	10.5920991304	0.0917531157703	0.364863459889	19.8912636836
-chr5	158592499	158592849	SUNP_109802	0	+	158.17672933	141.921773774	0.134352776664	0.118725411551	195.744322553
-chr6	4425299	4431999	SUNP_111239	0	+	109.679449913	78.4220476627	258.215007788	125.027604479	42.2950473615
-chr6	23940549	23944049	SUNP_112350	0	+	20.4528284495	59.9402732645	5.60251078687	0.985420915876	0.0833461227417
-chr6	25658199	25658649	SUNP_112441	0	-	249.539975801	182.576607005	0.104496604072	0.0923419867622	148.263491677
-chr6	26779299	26781249	SUNP_112472	0	+	13.9822151832	2.92408700356	29.154552536	0.340955028045	1.88063046186
-chr6	53082199	53084249	SUNP_113514	0	+	0.272644457468	0.327229248605	12.2261026764	0.689186535347	23.5605259165
-chr6	106779699	106786049	SUNP_116729	0	+	15.7193043604	13.0215033036	1.42921733285	0.968500207616	0.0328134341503
-chr6	133371449	133371649	SUNP_118187	0	-	7.27314044714	4.07283546925	0.940469436646	0.207769470215	62.7179573631
-chr6	147693499	147695149	SUNP_119052	0	-	27.6160024501	20.3956371567	0.0284990738377	0.0755525346236	41.1426769534
-chr6	160515099	160522199	SUNP_119708	0	-	105.856918349	76.683134756	0.311282137481	0.210695800781	9.17981239211
-chr6	165822349	165824699	SUNP_120052	0	+	45.9852137442	37.6053377578	135.547658805	53.5603170452	59.2998796698
-chr7	53431449	53433999	SUNP_123409	0	+	0.196704271728	1.20885389552	10.2898420715	0.847373525582	16.031871845
-chr7	145691949	145694599	SUNP_127964	0	+	54.0858277623	30.9131677718	93.3549001168	44.5645912717	13.1152200692
-chr8	4377249	4379899	SUNP_129007	0	+	10.7701155873	35.2948938334	1.59702357166	0.078403573666	1.36813446765
-chr8	34313649	34315699	SUNP_130571	0	-	91.5735832917	75.2938918695	0.0917531157703	0.0608105766482	31.610541674
-chr8	36088549	36089649	SUNP_130682	0	-	88.671731094	90.9527321902	8.33597909754	6.98860945268	33.2247952929
-chr8	59426999	59432849	SUNP_131857	0	+	15.998397942	12.2451262474	0.00803820031321	0.156271054521	10.8563667571
-chr9	75669699	75669849	SUNP_140288	0	+	1325.83737254	964.702989578	0.0	0.554051920573	419.5088178
-chr9	76717349	76720199	SUNP_140368	0	+	15.1107334154	0.605251091405	0.0	0.0145803136993	0.0
-chr9	110018249	110018899	SUNP_142250	0	-	1.9071668016	10.4677400296	0.0723438028189	0.191787203275	0.128224804218
-chrX	11678399	11678799	SUNP_144215	0	+	17.0542603588	44.6015413642	0.705352077484	1.86992523193	6.45932451248
-chrX	13683449	13687849	SUNP_144336	0	-	14.6684227513	27.3918150187	1.36795554421	2.37046077381	1.32596104362
-chrX	24820949	24824299	SUNP_144816	0	-	47.6826253504	35.7484581193	0.0280737145267	0.11163732728	21.1599634005
-chrX	102676249	102679449	SUNP_148801	0	-	0.111963368952	17.3644541636	0.0	0.0389567756653	0.0130228316784
-chrX	122184999	122185949	SUNP_149759	0	+	24.8308823977	20.9820378354	3.01940187555	0.0437409410979	4.21117251748
-chrX	150872299	150873799	SUNP_151471	0	-	108.808091931	85.5242208862	0.438885737101	0.443241536458	50.980045077
-chrY	5501699	5508249	SUNP_151888	0	-	15.2677694251	13.3773838553	0.0717915600493	0.0507528476861	9.47982617444

analysis/GRO_seq_TFSEE/.ipynb_checkpoints/Untitled-checkpoint.ipynb

+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 2
+}