T2T Encode Track Settings
 
T2T Encode Reanalysis   (All Expression and Regulation tracks)

Maximum display mode:       Reset to defaults   
Select view (Help):
Coverage ▾       Enrichment ▾       Macs2 Peaks ▾       Macs2 hg38 LO Peaks ▾      
Select subtracks by cell line and antibody:
 All
Cell Line
22Rv1
BE2C
C4-2B
Caco-2
HAP-1
HL-60
MG63
RWPE1
RWPE2
SJCRH30
SJSA1
VCaP
brain microvascular endothelial cell
epithelial cell of prostate male
Cell Line
All 
Antibody













Antibody
CTCF   CTCF
Control   Control
H3K27ac   H3K27ac
H3K27me3   H3K27me3
H3K36me3   H3K36me3
H3K4me1   H3K4me1
H3K4me3   H3K4me3
H3K9me3   H3K9me3
List subtracks: only selected/visible    all    ()
  Cell Line↓1 Antibody↓2 view↓3   Track Name↓4  
hide
 Configure
 22Rv1  Control  Coverage  22Rv1 Control Coverage   Schema 
hide
 Configure
 22Rv1  CTCF  Coverage  22Rv1 CTCF Coverage   Schema 
hide
 Configure
 22Rv1  CTCF  Enrichment  22Rv1 CTCF Enrichment   Schema 
hide
 Configure
 22Rv1  CTCF  Macs2 Peaks  22Rv1 CTCF Macs2 Peaks   Schema 
hide
 Configure
 22Rv1  CTCF  Macs2 hg38 LO Peaks  22Rv1 CTCF hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 22Rv1  H3K27ac  Coverage  22Rv1 H3K27ac Coverage   Schema 
hide
 Configure
 22Rv1  H3K27ac  Enrichment  22Rv1 H3K27ac Enrichment   Schema 
hide
 Configure
 22Rv1  H3K27ac  Macs2 Peaks  22Rv1 H3K27ac Macs2 Peaks   Schema 
hide
 Configure
 22Rv1  H3K27ac  Macs2 hg38 LO Peaks  22Rv1 H3K27ac hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 BE2C  Control  Coverage  BE2C Control Coverage   Schema 
hide
 Configure
 BE2C  H3K27me3  Coverage  BE2C H3K27me3 Coverage   Schema 
hide
 Configure
 BE2C  H3K27me3  Enrichment  BE2C H3K27me3 Enrichment   Schema 
hide
 Configure
 BE2C  H3K27me3  Macs2 Peaks  BE2C H3K27me3 Macs2 Peaks   Schema 
hide
 Configure
 BE2C  H3K27me3  Macs2 hg38 LO Peaks  BE2C H3K27me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 BE2C  H3K36me3  Coverage  BE2C H3K36me3 Coverage   Schema 
hide
 Configure
 BE2C  H3K36me3  Enrichment  BE2C H3K36me3 Enrichment   Schema 
hide
 Configure
 BE2C  H3K36me3  Macs2 Peaks  BE2C H3K36me3 Macs2 Peaks   Schema 
hide
 Configure
 BE2C  H3K36me3  Macs2 hg38 LO Peaks  BE2C H3K36me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 BE2C  H3K4me1  Coverage  BE2C H3K4me1 Coverage   Schema 
hide
 Configure
 BE2C  H3K4me1  Enrichment  BE2C H3K4me1 Enrichment   Schema 
hide
 Configure
 BE2C  H3K4me1  Macs2 Peaks  BE2C H3K4me1 Macs2 Peaks   Schema 
hide
 Configure
 BE2C  H3K4me1  Macs2 hg38 LO Peaks  BE2C H3K4me1 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 BE2C  H3K9me3  Coverage  BE2C H3K9me3 Coverage   Schema 
hide
 Configure
 BE2C  H3K9me3  Enrichment  BE2C H3K9me3 Enrichment   Schema 
hide
 Configure
 BE2C  H3K9me3  Macs2 Peaks  BE2C H3K9me3 Macs2 Peaks   Schema 
hide
 Configure
 BE2C  H3K9me3  Macs2 hg38 LO Peaks  BE2C H3K9me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 brain microvascular endothelial cell  Control  Coverage  brain_microvascular_endothelial_cell Control Coverage   Schema 
hide
 Configure
 brain microvascular endothelial cell  H3K27ac  Coverage  brain_microvascular_endothelial_cell H3K27ac Coverage   Schema 
hide
 Configure
 brain microvascular endothelial cell  H3K27ac  Enrichment  brain_microvascular_endothelial_cell H3K27ac Enrichment   Schema 
hide
 Configure
 brain microvascular endothelial cell  H3K27ac  Macs2 Peaks  brain_microvascular_endothelial_cell H3K27ac Macs2 Peaks   Schema 
hide
 Configure
 brain microvascular endothelial cell  H3K27ac  Macs2 hg38 LO Peaks  brain_microvascular_endothelial_cell H3K27ac hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 brain microvascular endothelial cell  H3K27me3  Coverage  brain_microvascular_endothelial_cell H3K27me3 Coverage   Schema 
hide
 Configure
 brain microvascular endothelial cell  H3K27me3  Enrichment  brain_microvascular_endothelial_cell H3K27me3 Enrichment   Schema 
hide
 Configure
 brain microvascular endothelial cell  H3K27me3  Macs2 Peaks  brain_microvascular_endothelial_cell H3K27me3 Macs2 Peaks   Schema 
hide
 Configure
 brain microvascular endothelial cell  H3K27me3  Macs2 hg38 LO Peaks  brain_microvascular_endothelial_cell H3K27me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 brain microvascular endothelial cell  H3K36me3  Coverage  brain_microvascular_endothelial_cell H3K36me3 Coverage   Schema 
hide
 Configure
 brain microvascular endothelial cell  H3K36me3  Enrichment  brain_microvascular_endothelial_cell H3K36me3 Enrichment   Schema 
hide
 Configure
 brain microvascular endothelial cell  H3K36me3  Macs2 Peaks  brain_microvascular_endothelial_cell H3K36me3 Macs2 Peaks   Schema 
hide
 Configure
 brain microvascular endothelial cell  H3K36me3  Macs2 hg38 LO Peaks  brain_microvascular_endothelial_cell H3K36me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 C4-2B  Control  Coverage  C4-2B Control Coverage   Schema 
hide
 Configure
 C4-2B  CTCF  Coverage  C4-2B CTCF Coverage   Schema 
hide
 Configure
 C4-2B  CTCF  Enrichment  C4-2B CTCF Enrichment   Schema 
hide
 Configure
 C4-2B  CTCF  Macs2 Peaks  C4-2B CTCF Macs2 Peaks   Schema 
hide
 Configure
 C4-2B  CTCF  Macs2 hg38 LO Peaks  C4-2B CTCF hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 C4-2B  H3K27ac  Coverage  C4-2B H3K27ac Coverage   Schema 
hide
 Configure
 C4-2B  H3K27ac  Enrichment  C4-2B H3K27ac Enrichment   Schema 
hide
 Configure
 C4-2B  H3K27ac  Macs2 Peaks  C4-2B H3K27ac Macs2 Peaks   Schema 
hide
 Configure
 C4-2B  H3K27ac  Macs2 hg38 LO Peaks  C4-2B H3K27ac hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 Caco-2  Control  Coverage  Caco-2 Control Coverage   Schema 
hide
 Configure
 Caco-2  H3K4me1  Coverage  Caco-2 H3K4me1 Coverage   Schema 
hide
 Configure
 Caco-2  H3K4me1  Enrichment  Caco-2 H3K4me1 Enrichment   Schema 
hide
 Configure
 Caco-2  H3K4me1  Macs2 Peaks  Caco-2 H3K4me1 Macs2 Peaks   Schema 
hide
 Configure
 Caco-2  H3K4me1  Macs2 hg38 LO Peaks  Caco-2 H3K4me1 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 Caco-2  H3K9me3  Coverage  Caco-2 H3K9me3 Coverage   Schema 
hide
 Configure
 Caco-2  H3K9me3  Enrichment  Caco-2 H3K9me3 Enrichment   Schema 
hide
 Configure
 Caco-2  H3K9me3  Macs2 Peaks  Caco-2 H3K9me3 Macs2 Peaks   Schema 
hide
 Configure
 Caco-2  H3K9me3  Macs2 hg38 LO Peaks  Caco-2 H3K9me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 epithelial cell of prostate male  Control  Coverage  epithelial_cell_of_prostate_male Control Coverage   Schema 
hide
 Configure
 epithelial cell of prostate male  CTCF  Coverage  epithelial_cell_of_prostate_male CTCF Coverage   Schema 
hide
 Configure
 epithelial cell of prostate male  CTCF  Enrichment  epithelial_cell_of_prostate_male CTCF Enrichment   Schema 
hide
 Configure
 epithelial cell of prostate male  CTCF  Macs2 Peaks  epithelial_cell_of_prostate_male CTCF Macs2 Peaks   Schema 
hide
 Configure
 epithelial cell of prostate male  CTCF  Macs2 hg38 LO Peaks  epithelial_cell_of_prostate_male CTCF hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 epithelial cell of prostate male  H3K27ac  Coverage  epithelial_cell_of_prostate_male H3K27ac Coverage   Schema 
hide
 Configure
 epithelial cell of prostate male  H3K27ac  Enrichment  epithelial_cell_of_prostate_male H3K27ac Enrichment   Schema 
hide
 Configure
 epithelial cell of prostate male  H3K27ac  Macs2 Peaks  epithelial_cell_of_prostate_male H3K27ac Macs2 Peaks   Schema 
hide
 Configure
 epithelial cell of prostate male  H3K27ac  Macs2 hg38 LO Peaks  epithelial_cell_of_prostate_male H3K27ac hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 HAP-1  Control  Coverage  HAP-1 Control Coverage   Schema 
hide
 Configure
 HAP-1  H3K27ac  Coverage  HAP-1 H3K27ac Coverage   Schema 
hide
 Configure
 HAP-1  H3K27ac  Enrichment  HAP-1 H3K27ac Enrichment   Schema 
hide
 Configure
 HAP-1  H3K27ac  Macs2 Peaks  HAP-1 H3K27ac Macs2 Peaks   Schema 
hide
 Configure
 HAP-1  H3K27ac  Macs2 hg38 LO Peaks  HAP-1 H3K27ac hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 HAP-1  H3K27me3  Coverage  HAP-1 H3K27me3 Coverage   Schema 
hide
 Configure
 HAP-1  H3K27me3  Enrichment  HAP-1 H3K27me3 Enrichment   Schema 
hide
 Configure
 HAP-1  H3K27me3  Macs2 Peaks  HAP-1 H3K27me3 Macs2 Peaks   Schema 
hide
 Configure
 HAP-1  H3K27me3  Macs2 hg38 LO Peaks  HAP-1 H3K27me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 HAP-1  H3K36me3  Coverage  HAP-1 H3K36me3 Coverage   Schema 
hide
 Configure
 HAP-1  H3K36me3  Enrichment  HAP-1 H3K36me3 Enrichment   Schema 
hide
 Configure
 HAP-1  H3K36me3  Macs2 Peaks  HAP-1 H3K36me3 Macs2 Peaks   Schema 
hide
 Configure
 HAP-1  H3K36me3  Macs2 hg38 LO Peaks  HAP-1 H3K36me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 HAP-1  H3K4me1  Coverage  HAP-1 H3K4me1 Coverage   Schema 
hide
 Configure
 HAP-1  H3K4me1  Enrichment  HAP-1 H3K4me1 Enrichment   Schema 
hide
 Configure
 HAP-1  H3K4me1  Macs2 Peaks  HAP-1 H3K4me1 Macs2 Peaks   Schema 
hide
 Configure
 HAP-1  H3K4me1  Macs2 hg38 LO Peaks  HAP-1 H3K4me1 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 HAP-1  H3K4me3  Coverage  HAP-1 H3K4me3 Coverage   Schema 
hide
 Configure
 HAP-1  H3K4me3  Enrichment  HAP-1 H3K4me3 Enrichment   Schema 
hide
 Configure
 HAP-1  H3K4me3  Macs2 Peaks  HAP-1 H3K4me3 Macs2 Peaks   Schema 
hide
 Configure
 HAP-1  H3K4me3  Macs2 hg38 LO Peaks  HAP-1 H3K4me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 HAP-1  H3K9me3  Coverage  HAP-1 H3K9me3 Coverage   Schema 
hide
 Configure
 HAP-1  H3K9me3  Enrichment  HAP-1 H3K9me3 Enrichment   Schema 
hide
 Configure
 HAP-1  H3K9me3  Macs2 Peaks  HAP-1 H3K9me3 Macs2 Peaks   Schema 
hide
 Configure
 HAP-1  H3K9me3  Macs2 hg38 LO Peaks  HAP-1 H3K9me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 HL-60  Control  Coverage  HL-60 Control Coverage   Schema 
hide
 Configure
 HL-60  H3K27ac  Coverage  HL-60 H3K27ac Coverage   Schema 
hide
 Configure
 HL-60  H3K27ac  Enrichment  HL-60 H3K27ac Enrichment   Schema 
hide
 Configure
 HL-60  H3K27ac  Macs2 Peaks  HL-60 H3K27ac Macs2 Peaks   Schema 
hide
 Configure
 HL-60  H3K27ac  Macs2 hg38 LO Peaks  HL-60 H3K27ac hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 MG63  Control  Coverage  MG63 Control Coverage   Schema 
hide
 Configure
 MG63  H3K27me3  Coverage  MG63 H3K27me3 Coverage   Schema 
hide
 Configure
 MG63  H3K27me3  Enrichment  MG63 H3K27me3 Enrichment   Schema 
hide
 Configure
 MG63  H3K27me3  Macs2 Peaks  MG63 H3K27me3 Macs2 Peaks   Schema 
hide
 Configure
 MG63  H3K27me3  Macs2 hg38 LO Peaks  MG63 H3K27me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 MG63  H3K36me3  Coverage  MG63 H3K36me3 Coverage   Schema 
hide
 Configure
 MG63  H3K36me3  Enrichment  MG63 H3K36me3 Enrichment   Schema 
hide
 Configure
 MG63  H3K36me3  Macs2 Peaks  MG63 H3K36me3 Macs2 Peaks   Schema 
hide
 Configure
 MG63  H3K36me3  Macs2 hg38 LO Peaks  MG63 H3K36me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 MG63  H3K4me3  Coverage  MG63 H3K4me3 Coverage   Schema 
hide
 Configure
 MG63  H3K4me3  Enrichment  MG63 H3K4me3 Enrichment   Schema 
hide
 Configure
 MG63  H3K4me3  Macs2 Peaks  MG63 H3K4me3 Macs2 Peaks   Schema 
hide
 Configure
 MG63  H3K4me3  Macs2 hg38 LO Peaks  MG63 H3K4me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 MG63  H3K9me3  Coverage  MG63 H3K9me3 Coverage   Schema 
hide
 Configure
 MG63  H3K9me3  Enrichment  MG63 H3K9me3 Enrichment   Schema 
hide
 Configure
 MG63  H3K9me3  Macs2 Peaks  MG63 H3K9me3 Macs2 Peaks   Schema 
hide
 Configure
 MG63  H3K9me3  Macs2 hg38 LO Peaks  MG63 H3K9me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 RWPE1  Control  Coverage  RWPE1 Control Coverage   Schema 
hide
 Configure
 RWPE1  CTCF  Coverage  RWPE1 CTCF Coverage   Schema 
hide
 Configure
 RWPE1  CTCF  Enrichment  RWPE1 CTCF Enrichment   Schema 
hide
 Configure
 RWPE1  CTCF  Macs2 Peaks  RWPE1 CTCF Macs2 Peaks   Schema 
hide
 Configure
 RWPE1  CTCF  Macs2 hg38 LO Peaks  RWPE1 CTCF hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 RWPE1  H3K27ac  Coverage  RWPE1 H3K27ac Coverage   Schema 
hide
 Configure
 RWPE1  H3K27ac  Enrichment  RWPE1 H3K27ac Enrichment   Schema 
hide
 Configure
 RWPE1  H3K27ac  Macs2 Peaks  RWPE1 H3K27ac Macs2 Peaks   Schema 
hide
 Configure
 RWPE1  H3K27ac  Macs2 hg38 LO Peaks  RWPE1 H3K27ac hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 RWPE2  Control  Coverage  RWPE2 Control Coverage   Schema 
hide
 Configure
 RWPE2  CTCF  Coverage  RWPE2 CTCF Coverage   Schema 
hide
 Configure
 RWPE2  CTCF  Enrichment  RWPE2 CTCF Enrichment   Schema 
hide
 Configure
 RWPE2  CTCF  Macs2 Peaks  RWPE2 CTCF Macs2 Peaks   Schema 
hide
 Configure
 RWPE2  CTCF  Macs2 hg38 LO Peaks  RWPE2 CTCF hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 RWPE2  H3K27ac  Coverage  RWPE2 H3K27ac Coverage   Schema 
hide
 Configure
 RWPE2  H3K27ac  Enrichment  RWPE2 H3K27ac Enrichment   Schema 
hide
 Configure
 RWPE2  H3K27ac  Macs2 Peaks  RWPE2 H3K27ac Macs2 Peaks   Schema 
hide
 Configure
 RWPE2  H3K27ac  Macs2 hg38 LO Peaks  RWPE2 H3K27ac hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 RWPE2  H3K36me3  Coverage  RWPE2 H3K36me3 Coverage   Schema 
hide
 Configure
 RWPE2  H3K36me3  Enrichment  RWPE2 H3K36me3 Enrichment   Schema 
hide
 Configure
 RWPE2  H3K36me3  Macs2 Peaks  RWPE2 H3K36me3 Macs2 Peaks   Schema 
hide
 Configure
 RWPE2  H3K36me3  Macs2 hg38 LO Peaks  RWPE2 H3K36me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 SJCRH30  Control  Coverage  SJCRH30 Control Coverage   Schema 
hide
 Configure
 SJCRH30  H3K27ac  Coverage  SJCRH30 H3K27ac Coverage   Schema 
hide
 Configure
 SJCRH30  H3K27ac  Enrichment  SJCRH30 H3K27ac Enrichment   Schema 
hide
 Configure
 SJCRH30  H3K27ac  Macs2 Peaks  SJCRH30 H3K27ac Macs2 Peaks   Schema 
hide
 Configure
 SJCRH30  H3K27ac  Macs2 hg38 LO Peaks  SJCRH30 H3K27ac hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 SJCRH30  H3K27me3  Coverage  SJCRH30 H3K27me3 Coverage   Schema 
hide
 Configure
 SJCRH30  H3K27me3  Enrichment  SJCRH30 H3K27me3 Enrichment   Schema 
hide
 Configure
 SJCRH30  H3K27me3  Macs2 Peaks  SJCRH30 H3K27me3 Macs2 Peaks   Schema 
hide
 Configure
 SJCRH30  H3K27me3  Macs2 hg38 LO Peaks  SJCRH30 H3K27me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 SJCRH30  H3K36me3  Coverage  SJCRH30 H3K36me3 Coverage   Schema 
hide
 Configure
 SJCRH30  H3K36me3  Enrichment  SJCRH30 H3K36me3 Enrichment   Schema 
hide
 Configure
 SJCRH30  H3K36me3  Macs2 Peaks  SJCRH30 H3K36me3 Macs2 Peaks   Schema 
hide
 Configure
 SJCRH30  H3K36me3  Macs2 hg38 LO Peaks  SJCRH30 H3K36me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 SJCRH30  H3K4me1  Coverage  SJCRH30 H3K4me1 Coverage   Schema 
hide
 Configure
 SJCRH30  H3K4me1  Enrichment  SJCRH30 H3K4me1 Enrichment   Schema 
hide
 Configure
 SJCRH30  H3K4me1  Macs2 Peaks  SJCRH30 H3K4me1 Macs2 Peaks   Schema 
hide
 Configure
 SJCRH30  H3K4me1  Macs2 hg38 LO Peaks  SJCRH30 H3K4me1 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 SJCRH30  H3K4me3  Coverage  SJCRH30 H3K4me3 Coverage   Schema 
hide
 Configure
 SJCRH30  H3K4me3  Enrichment  SJCRH30 H3K4me3 Enrichment   Schema 
hide
 Configure
 SJCRH30  H3K4me3  Macs2 Peaks  SJCRH30 H3K4me3 Macs2 Peaks   Schema 
hide
 Configure
 SJCRH30  H3K4me3  Macs2 hg38 LO Peaks  SJCRH30 H3K4me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 SJCRH30  H3K9me3  Coverage  SJCRH30 H3K9me3 Coverage   Schema 
hide
 Configure
 SJCRH30  H3K9me3  Enrichment  SJCRH30 H3K9me3 Enrichment   Schema 
hide
 Configure
 SJCRH30  H3K9me3  Macs2 Peaks  SJCRH30 H3K9me3 Macs2 Peaks   Schema 
hide
 Configure
 SJCRH30  H3K9me3  Macs2 hg38 LO Peaks  SJCRH30 H3K9me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 SJSA1  Control  Coverage  SJSA1 Control Coverage   Schema 
hide
 Configure
 SJSA1  H3K27ac  Coverage  SJSA1 H3K27ac Coverage   Schema 
hide
 Configure
 SJSA1  H3K27ac  Enrichment  SJSA1 H3K27ac Enrichment   Schema 
hide
 Configure
 SJSA1  H3K27ac  Macs2 Peaks  SJSA1 H3K27ac Macs2 Peaks   Schema 
hide
 Configure
 SJSA1  H3K27ac  Macs2 hg38 LO Peaks  SJSA1 H3K27ac hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 SJSA1  H3K27me3  Coverage  SJSA1 H3K27me3 Coverage   Schema 
hide
 Configure
 SJSA1  H3K27me3  Enrichment  SJSA1 H3K27me3 Enrichment   Schema 
hide
 Configure
 SJSA1  H3K27me3  Macs2 Peaks  SJSA1 H3K27me3 Macs2 Peaks   Schema 
hide
 Configure
 SJSA1  H3K27me3  Macs2 hg38 LO Peaks  SJSA1 H3K27me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 SJSA1  H3K36me3  Coverage  SJSA1 H3K36me3 Coverage   Schema 
hide
 Configure
 SJSA1  H3K36me3  Enrichment  SJSA1 H3K36me3 Enrichment   Schema 
hide
 Configure
 SJSA1  H3K36me3  Macs2 Peaks  SJSA1 H3K36me3 Macs2 Peaks   Schema 
hide
 Configure
 SJSA1  H3K36me3  Macs2 hg38 LO Peaks  SJSA1 H3K36me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 SJSA1  H3K4me3  Coverage  SJSA1 H3K4me3 Coverage   Schema 
hide
 Configure
 SJSA1  H3K4me3  Enrichment  SJSA1 H3K4me3 Enrichment   Schema 
hide
 Configure
 SJSA1  H3K4me3  Macs2 Peaks  SJSA1 H3K4me3 Macs2 Peaks   Schema 
hide
 Configure
 SJSA1  H3K4me3  Macs2 hg38 LO Peaks  SJSA1 H3K4me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 SJSA1  H3K9me3  Coverage  SJSA1 H3K9me3 Coverage   Schema 
hide
 Configure
 SJSA1  H3K9me3  Enrichment  SJSA1 H3K9me3 Enrichment   Schema 
hide
 Configure
 SJSA1  H3K9me3  Macs2 Peaks  SJSA1 H3K9me3 Macs2 Peaks   Schema 
hide
 Configure
 SJSA1  H3K9me3  Macs2 hg38 LO Peaks  SJSA1 H3K9me3 hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 VCaP  Control  Coverage  VCaP Control Coverage   Schema 
hide
 Configure
 VCaP  CTCF  Coverage  VCaP CTCF Coverage   Schema 
hide
 Configure
 VCaP  CTCF  Enrichment  VCaP CTCF Enrichment   Schema 
hide
 Configure
 VCaP  CTCF  Macs2 Peaks  VCaP CTCF Macs2 Peaks   Schema 
hide
 Configure
 VCaP  CTCF  Macs2 hg38 LO Peaks  VCaP CTCF hg38 liftover Macs2 Peaks   Schema 
hide
 Configure
 VCaP  H3K27ac  Coverage  VCaP H3K27ac Coverage   Schema 
hide
 Configure
 VCaP  H3K27ac  Enrichment  VCaP H3K27ac Enrichment   Schema 
hide
 Configure
 VCaP  H3K27ac  Macs2 Peaks  VCaP H3K27ac Macs2 Peaks   Schema 
hide
 Configure
 VCaP  H3K27ac  Macs2 hg38 LO Peaks  VCaP H3K27ac hg38 liftover Macs2 Peaks   Schema 
    

Description

These tracks represent a reanalysis of ENCODE data against the T2T chm13 genome. All ChIP-seq experiments with pair-end data and read lengths of 100bp or greater are included.

Track types include:

  • Coverage pileups of mapped and filtered reads
  • Enrichment of mapped reads relative to a control
  • ChIP-seq peaks as called by MACS2
  • ChIP-seq peaks as called by MACS2 in GRCh38 and lifted over to chm13

Methods

Prior to mapping, reads originating from a single library were combined. Reads were mapped with Bowtie2 (v2.4.1) as paired-end with the arguments "--no-discordant --no-mixed --very-sensitive --no-unal --omit-sec-seq --xeq --reorder". Alignments were filtered using SAMtools (v1.10) using the arguments "-F 1804 -f 2 -q 2" to remove unmapped or single end mapped reads and those with a mapping quality score less than 2. PCR duplicates were identified and removed with the Picard tools "mark duplicates" command (v2.22.1) and the arguments "VALIDATION_STRINGENCY=LENIENT ASSUME_SORT_ORDER=queryname REMOVE_DUPLICATES = true".

Alignments were then filtered for the presence of unique k-mers. Specifically, for each alignment, reference sequences aligned with template ends were compared to a database of minimum unique k-mer lengths. The size of the k-mers in the k-mer filtering step are dependent on the length of the mapped reference sequence. Alignments were discarded if no unique k-mers occurred in either end of the read. The minimum unique k-mer length database was generated using scripts found here. Alignments from replicates were then pooled.

Bigwig coverage tracks were created using deepTools bamCoverage (v3.4.3) with a bin size of 1bp and default for all other parameters. Enrichment tracks were created using deepTools bamCompare with a bin size of 50bp, a pseudo-count of 1, and excluding bins with zero counts in both target and control tracks.

Peak calls were made using MACS2 (v2.2.7.1) with default parameters and estimated genome sizes 3.03e9 and 2.79e9 for chm13 and GRCh38, respectively. GRCh38 peak calls were lifted over to chm13 using the UCSC liftOver utility, the chain file created by the T2T consortium, and the parameter "-minMatch=0.2".

Credits

Data were processed by Michael Sauria at Johns Hopkins University. For inquiries, please contact us at the following address: msauria@jhu.edu

References

Gershman A, Sauria MEG, Guitart X, Vollger MR, Hook PW, Hoyt SJ, Jain M, Shumate A, Razaghi R, Koren S, Altemose N, Caldas GV, Logsdon GA, Rhie A, Eichler EE, Schatz MC, O'Neill RJ, Phillippy AM, Miga KH, Timp W. Epigenetic patterns in a complete human genome. Science. 2022 Apr;376(6588):eabj5089. doi: 10.1126/science.abj5089. Epub 2022 Apr 1. PMID: 35357915.