Peak calls on imputed data


Macs2 (version. 2.0.10) was used to call peaks on the imputed signal data. The bdgpeakcall command was used to generate narrowPeaks while the bdgbroadcall command was used to generate gappedPeaks with the '-c' cutoff flag set to 2. The peak calls are reported in a three column bed format.

Chromatin state model based on imputed data (25 state, 12 marks, 127 epigenomes)


The states are as follows

1TssAActive TSSRed255,0,0
2PromUPromoter Upstream TSSOrange Red255,69,0
3PromD1Promoter Downstream TSS 1Orange Red255,69,0
4PromD2Promoter Downstream TSS 2Orange Red255,69,0
5Tx5’Transcribed - 5' preferentialGreen0,128,0
6TxStrong transcriptionGreen0,128,0
7Tx3’Transcribed - 3' preferentialGreen0,128,0
8TxWkWeak transcriptionLighter Green0,150,0
9TxRegTranscribed & regulatory (Prom/Enh)Electric Lime194,225,5
10TxEnh5’Transcribed 5' preferential and EnhElectric Lime194,225,5
11TxEnh3’Transcribed 3' preferential and EnhElectric Lime194,225,5
12TxEnhWTranscribed and Weak EnhancerElectric Lime194,225,5
13EnhA1Active Enhancer 1Orange255,195,77
14EnhA2Active Enhancer 2Orange255,195,77
15EnhAFActive Enhancer FlankOrange255,195,77
16EnhW1Weak Enhancer 1Yellow255,255,0
17EnhW2Weak Enhancer 2Yellow255,255,0
18EnhAcPrimary H3K27ac possible EnhancerYellow255,255,0
19DNasePrimary DNaseLemon255,255,102
20ZNF/RptsZNF genes & repeatsAquamarine102,205,170
21HetHeterochromatinLight Purple138,145,208
22PromPPoised PromoterPink230,184,183
23PromBivBivalent PromoterDark Purple112,48,160
24ReprPCRepressed PolycombGray128,128,128

A chromatin state model based on the imputed data for 12 marks, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K27ac, H4K20me1, H3K79me2, H3K36me3, H3K9me3, H3K27me3, H2A.Z, and DNase, across all 127 reference epigenomes with 25-states was learned. Within the directory for this model one can find both plain bed files containing the segmentation information and versions that can be viewed in the browser. An additional chromatin state model based on 29-marks across just the seven class 1 reference epigenomes was also learned.