### ============================================================================
### ATAC-seq
###

track ATAC-seq
compositeTrack on
visibility full
# NOTE: "[A-Z]_" prefix on subGroup tags is to manually set sortOrder
subGroup1 view Views \
  A_CPM=ATAC-seq_CPM \
  B_OCR=Open_chromatin_regions \
  C_DAR=Differentially_accessible_regions
subGroup2 NeuN NeuN_status \
  A_pos=NeuN+ \
  B_neg=NeuN- \
  C_unsorted=Unsorted \
  D_union=Union \
  E_NA=Not_applicable
subGroup3 Tissue Brain_region \
  A_BA9=Dorsolateral_prefrontal_cortex \
  B_BA24=Anterior_cingulate_gyrus \
  C_HC=Hippocampus \
  D_NAcc=Nucleus_accumbens \
  E_union=Union \
  F_NA=Not_applicable
subGroup4 Comparison Comparison \
  A_pos=Between_brain_regions_in_NeuN+_samples \
  B_neg=Between_brain_regions_in_NeuN-_samples \
  C_pos_vs_neg=Between_NeuN+_and_NeuN-_samples \
  D_NAcc_pos_vs_BA9_pos=Between_NAcc_(NeuN+)_and_BA9_(NeuN+)_samples \
  E_unsorted=Between_brain_regions_in_unsorted_samples \
  F_NA=Not_applicable
dimensions dimX=Tissue dimY=NeuN dimA=Comparison
filterComposite dimA
sortOrder NeuN=+ Tissue=+ Comparison=+ view=+
type bed 3
shortLabel ATAC-seq
longLabel ATAC-seq CPM, OCRs, and DARs
priority 4
html docs/ATAC-seq

  track OCRs
  parent ATAC-seq on
  shortLabel OCRs
  longLabel Open chromatin regions (OCRs)
  view B_OCR
  visibility hide
  type bigBed 9
  viewUi off

    track OCRs.BA9_neg
    parent OCRs off
    subGroups NeuN=B_neg Tissue=A_BA9 Comparison=F_NA view=B_OCR
    bigDataUrl OCRs.BA9_neg.bb
    shortLabel OCRs (BA9-)
    longLabel OCRs in BA9 (NeuN-) samples
    type bigBed 9
    itemRgb on

    track OCRs.NAcc_neg
    parent OCRs off
    subGroups NeuN=B_neg Tissue=D_NAcc Comparison=F_NA view=B_OCR
    bigDataUrl OCRs.NAcc_neg.bb
    shortLabel OCRs (NAcc-)
    longLabel OCRs in NAcc (NeuN-) samples
    type bigBed 9
    itemRgb on

    track OCRs.BA9_pos
    parent OCRs off
    subGroups NeuN=A_pos Tissue=A_BA9 Comparison=F_NA view=B_OCR
    bigDataUrl OCRs.BA9_pos.bb
    shortLabel OCRs (BA9+)
    longLabel OCRs in BA9 (NeuN+) samples
    type bigBed 9
    itemRgb on

    track OCRs.NAcc_pos
    parent OCRs off
    subGroups NeuN=A_pos Tissue=D_NAcc Comparison=F_NA view=B_OCR
    bigDataUrl OCRs.NAcc_pos.bb
    shortLabel OCRs (NAcc+)
    longLabel OCRs in NAcc (NeuN+) samples
    type bigBed 9
    itemRgb on

    track OCR.union
    parent OCRs off
    subGroups NeuN=D_union Tissue=E_union Comparison=F_NA view=B_OCR
    bigDataUrl OCRs.union.bb
    shortLabel OCRs (union)
    longLabel Union of OCRs across all samples
    type bigBed 9
    itemRgb on

  track DARs
  parent ATAC-seq on
  shortLabel DARs
  longLabel Differentially accessible regions (DARs)
  view C_DAR
  visibility squish
  type bigBed
  viewUi on

    track DARs.pos_vs_neg
    parent DARs off
    subGroups NeuN=E_NA Tissue=F_NA Comparison=C_pos_vs_neg view=C_DAR
    bigDataUrl DARs.pos_vs_neg.bb
    shortLabel DARs (+ vs -)
    longLabel DARs between NeuN+ and NeuN- samples
    type bigBed

    track DARs.NAcc_pos_vs_BA9_pos
    parent DARs on
    subGroups NeuN=A_pos Tissue=F_NA Comparison=A_pos view=C_DAR
    bigDataUrl DARs.NAcc_pos_vs_BA9_pos.bb
    shortLabel DARs (+)
    longLabel DARs between NAcc (NeuN+) and BA9 (NeuN+) samples
    type bigBed

    track DARs.NAcc_neg_vs_BA9_neg
    parent DARs off
    subGroups NeuN=B_neg Tissue=F_NA Comparison=B_neg view=C_DAR
    bigDataUrl DARs.NAcc_neg_vs_BA9_neg.bb
    shortLabel DARs (-)
    longLabel DARs between NAcc (NeuN-) and BA9 (NeuN-) samples
    type bigBed

  track ATAC-seq_CPM
  parent ATAC-seq on
  shortLabel ATAC-seq CPM
  longLabel Average ATAC-seq counts per million (CPM)
  view A_CPM
  visibility full
  type bigWig
  viewUi on
  # NOTE: viewLimits were chosen by trial and error. They happen to roughly
  #       coincide with the 0.99 quantile of non-zero CPM in NAcc_pos
  viewLimits 0:0.1

    track BA9_neg.ATAC-seq.cpm
    parent ATAC-seq_CPM off
    subGroups NeuN=B_neg Tissue=A_BA9 Comparison=F_NA view=A_CPM
    bigDataUrl BA9_neg.ATAC-seq.cpm.bw
    shortLabel ATAC CPM (BA9-)
    longLabel Average ATAC-seq CPM in BA9 (NeuN-) samples
    type bigWig
    color 0,191,255
    maxHeightPixels 100:30:8

    track NAcc_neg.ATAC-seq.cpm
    parent ATAC-seq_CPM off
    subGroups NeuN=B_neg Tissue=D_NAcc Comparison=F_NA view=A_CPM
    bigDataUrl NAcc_neg.ATAC-seq.cpm.bw
    shortLabel ATAC CPM (NAcc-)
    longLabel Average ATAC-seq CPM in NAcc (NeuN-) samples
    type bigWig
    color 255,127,36
    maxHeightPixels 100:30:8

    track BA9_pos.ATAC-seq.cpm
    parent ATAC-seq_CPM on
    subGroups NeuN=A_pos Tissue=A_BA9 Comparison=F_NA view=A_CPM
    bigDataUrl BA9_pos.ATAC-seq.cpm.bw
    shortLabel ATAC CPM (BA9+)
    longLabel Average ATAC-seq CPM in BA9 (NeuN+) samples
    type bigWig
    color 0,191,255
    maxHeightPixels 100:30:8

    track NAcc_pos.ATAC-seq.cpm
    parent ATAC-seq_CPM on
    subGroups NeuN=A_pos Tissue=D_NAcc Comparison=F_NA view=A_CPM
    bigDataUrl NAcc_neg.ATAC-seq.cpm.bw
    shortLabel ATAC CPM (NAcc+)
    longLabel Average ATAC-seq CPM in NAcc (NeuN+) samples
    type bigWig
    color 255,127,36
    maxHeightPixels 100:30:8

### ============================================================================
### RNA-seq
###

track RNA-seq
compositeTrack on
visibility full
# NOTE: "[A-Z]_" prefix on subGroup tags is to manually set sortOrder
subGroup1 view Views \
  A_CPM=RNA-seq_CPM \
  B_DEG=Differentially_expressed_genes
subGroup2 NeuN NeuN_status \
  A_pos=NeuN+ \
  B_neg=NeuN- \
  C_unsorted=Unsorted \
  D_union=Union \
  E_NA=Not_applicable
subGroup3 Tissue Brain_region \
  A_BA9=Dorsolateral_prefrontal_cortex \
  B_BA24=Anterior_cingulate_gyrus \
  C_HC=Hippocampus \
  D_NAcc=Nucleus_accumbens \
  E_union=Union \
  F_NA=Not_applicable
subGroup4 Comparison Comparison \
  A_pos=Between_brain_regions_in_NeuN+_samples \
  B_neg=Between_brain_regions_in_NeuN-_samples \
  C_pos_vs_neg=Between_NeuN+_and_NeuN-_samples \
  D_NAcc_pos_vs_BA9_pos=Between_NAcc_(NeuN+)_and_BA9_(NeuN+)_samples \
  E_unsorted=Between_brain_regions_in_unsorted_samples \
  F_NA=Not_applicable
dimensions dimX=Tissue dimY=NeuN dimA=Comparison
filterComposite dimA
sortOrder NeuN=+ Tissue=+ Comparison=+ view=+
type bed 3
shortLabel RNA-seq
longLabel RNA-seq CPM and DEGs
priority 5
html docs/RNA-seq

  track DEGs
  parent RNA-seq on
  shortLabel DEGs
  longLabel Differentially expressed genes (DEGs) from RNA-sequencing data
  view B_DEG
  visibility squish
  type bigBed
  viewUi on

    track DEGs.pos_vs_neg
    parent DEGs off
    subGroups NeuN=E_NA Tissue=F_NA Comparison=C_pos_vs_neg view=B_DEG
    bigDataUrl DEGs.pos_vs_neg.bb
    shortLabel DEGs (+ vs -)
    longLabel DEGs between NeuN+ and NeuN- samples
    type bigBed

    track DEGs.NAcc_pos_vs_BA9_pos
    parent DEGs on
    subGroups NeuN=A_pos Tissue=F_NA Comparison=A_pos view=B_DEG
    bigDataUrl DEGs.NAcc_pos_vs_BA9_pos.bb
    shortLabel DEGs (+)
    longLabel DEGs between NAcc (NeuN+) and BA9 (NeuN+)
    type bigBed

    track DEGs.NAcc_neg_vs_BA9_neg
    parent DEGs off
    subGroups NeuN=B_neg Tissue=F_NA Comparison=B_neg view=B_DEG
    bigDataUrl DEGs.NAcc_neg_vs_BA9_neg.bb
    shortLabel DEGs (-)
    longLabel DEGs between NAcc (NeuN-) and BA9 (NeuN-)
    type bigBed

  track RNA-seq_CPM
  parent RNA-seq on
  shortLabel RNA-seq CPM
  longLabel Average RNA-seq counts per million (CPM)
  view A_CPM
  visibility full
  type bigWig
  viewUi on
  # NOTE: viewLimits were chosen by trial and error. They happen to roughly
  #       coincide with the 0.99 quantile of non-zero CPM in NAcc_pos
  viewLimits 0:1

    track BA9_neg.RNA-seq.cpm
    parent RNA-seq_CPM off
    subGroups NeuN=B_neg Tissue=A_BA9 Comparison=F_NA view=A_CPM
    bigDataUrl BA9_neg.RNA-seq.cpm.bw
    shortLabel RNA CPM (BA9-)
    longLabel Average RNA-seq CPM in BA9 (NeuN-) samples
    type bigWig
    color 0,191,255
    maxHeightPixels 100:30:8

    track NAcc_neg.RNA-seq.cpm
    parent RNA-seq_CPM off
    subGroups NeuN=B_neg Tissue=D_NAcc Comparison=F_NA view=A_CPM
    bigDataUrl NAcc_neg.RNA-seq.cpm.bw
    shortLabel RNA CPM (NAcc-)
    longLabel Average RNA-seq CPM in NAcc (NeuN-) samples
    type bigWig
    color 255,127,36
    maxHeightPixels 100:30:8

    track BA9_pos.RNA-seq.cpm
    parent RNA-seq_CPM on
    subGroups NeuN=A_pos Tissue=A_BA9 Comparison=F_NA view=A_CPM
    bigDataUrl BA9_pos.RNA-seq.cpm.bw
    shortLabel RNA CPM (BA9+)
    longLabel Average RNA-seq CPM in BA9 (NeuN+) samples
    type bigWig
    color 0,191,255
    maxHeightPixels 100:30:8

    track NAcc_pos.RNA-seq.cpm
    parent RNA-seq_CPM on
    subGroups NeuN=A_pos Tissue=D_NAcc Comparison=F_NA view=A_CPM
    bigDataUrl NAcc_neg.RNA-seq.cpm.bw
    shortLabel RNA CPM (NAcc+)
    longLabel Average RNA-seq CPM in NAcc (NeuN+) samples
    type bigWig
    color 255,127,36
    maxHeightPixels 100:30:8

### ============================================================================
### mCG
###

track WGBS_mCG
compositeTrack on
visibility full
# NOTE: "[A-Z]_" prefix on subGroup tags is to manually set sortOrder
subGroup1 view Views \
  A_mCG=mCG \
  B_CG-DMR=Differentially_methylated_regions
subGroup2 NeuN NeuN_status \
  A_pos=NeuN+ \
  B_neg=NeuN- \
  C_unsorted=Unsorted \
  D_union=Union \
  E_NA=Not_applicable
subGroup3 Tissue Brain_region \
  A_BA9=Dorsolateral_prefrontal_cortex \
  B_BA24=Anterior_cingulate_gyrus \
  C_HC=Hippocampus \
  D_NAcc=Nucleus_accumbens \
  E_union=Union \
  F_NA=Not_applicable
subGroup4 Comparison Comparison \
  A_pos=Between_brain_regions_in_NeuN+_samples \
  B_neg=Between_brain_regions_in_NeuN-_samples \
  C_pos_vs_neg=Between_NeuN+_and_NeuN-_samples \
  D_NAcc_pos_vs_BA9_pos=Between_NAcc_(NeuN+)_and_BA9_(NeuN+)_samples \
  E_unsorted=Between_brain_regions_in_unsorted_samples \
  F_NA=Not_applicable
subGroup5 Smooth Smoothing_bandwidth \
  A_small=Small \
  B_large=Large
dimensions dimX=Tissue dimY=NeuN dimA=Comparison dimB=Smooth
filterComposite dimA
filterComposite dimB
sortOrder NeuN=+ Tissue=+ Comparison=+ Smooth=+ view=+
type bed 3
shortLabel WGBS (mCG)
longLabel Average mCG in each condition and CG-DMRs
priority 1
html docs/WGBS

  track DMRs
  parent WGBS_mCG on
  shortLabel CG-DMRs
  longLabel Differentially methylated regions using CpGs (CG-DMRs)
  view B_CG-DMR
  visibility squish
  type bigBed
  viewUi on

    track CG_DMRs.unsorted
    parent DMRs off
    subGroups NeuN=C_unsorted Tissue=F_NA Smooth=A_small Comparison=E_unsorted view=B_CG-DMR
    bigDataUrl CG-DMRs.unsorted.bb
    shortLabel CG-DMRs (bulk)
    longLabel CG-DMRs between brain regions in unsorted samples
    type bigBed

    track CG_DMRs.pos_vs_neg
    parent DMRs off
    subGroups NeuN=E_NA Tissue=F_NA Smooth=A_small Comparison=C_pos_vs_neg view=B_CG-DMR
    bigDataUrl CG-DMRs.pos_vs_neg.bb
    shortLabel CG-DMRs (+ vs -)
    longLabel CG-DMRs between NeuN+ and NeuN- samples
    type bigBed

    track CG_DMRs.pos
    parent DMRs on
    subGroups NeuN=A_pos Tissue=F_NA Smooth=A_small Comparison=A_pos view=B_CG-DMR
    bigDataUrl CG-DMRs.pos.bb
    shortLabel CG-DMRs (+)
    longLabel CG-DMRs between brain regions in NeuN+ samples
    type bigBed
    priority 1

    track CG_DMRs.NAcc_pos_vs_BA9_pos
    parent DMRs off
    subGroups NeuN=A_pos Tissue=F_NA Smooth=A_small Comparison=D_NAcc_pos_vs_BA9_pos view=B_CG-DMR
    bigDataUrl CG-DMRs.NAcc_pos_vs_BA9_pos.bb
    shortLabel DMRs (NAcc+BA9+)
    longLabel CG-DMRs between NAcc (NeuN+) and BA9 (NeuN+) samples
    type bigBed

    track CG_DMRs.neg
    parent DMRs off
    subGroups NeuN=B_neg Tissue=F_NA Smooth=A_small Comparison=B_neg view=B_CG-DMR
    bigDataUrl CG-DMRs.neg.bb
    shortLabel CG-DMRs (-)
    longLabel CG-DMRs between brain regions in NeuN- samples
    type bigBed

    track CG_blocks.pos_vs_neg
    parent DMRs off
    subGroups NeuN=E_NA Tissue=F_NA Smooth=B_large Comparison=C_pos_vs_neg view=B_CG-DMR
    bigDataUrl CG-blocks.pos_vs_neg.bb
    shortLabel CG-blocks (+vs-)
    longLabel CG-blocks between NeuN+ and NeuN- samples
    type bigBed

    track CG_blocks.pos
    parent DMRs off
    subGroups NeuN=A_pos Tissue=F_NA Smooth=B_large Comparison=A_pos view=B_CG-DMR
    bigDataUrl CG-blocks.pos.bb
    shortLabel CG-blocks (+)
    longLabel CG-blocks between brain regions in NeuN+ samples
    type bigBed

  track mCG
  parent WGBS_mCG on
  shortLabel mCG small smooth
  longLabel Average mCG (small smooth) in each condition
  view A_mCG
  visibility full
  type bigBed
  viewUi on
  viewLimits 0:1

    track BA24_pos.small_smooth.mCG
    parent mCG off
    subGroups NeuN=A_pos Tissue=B_BA24 Smooth=A_small Comparison=F_NA view=A_mCG
    bigDataUrl BA24_pos.small_smooth.mCG.bw
    shortLabel mCG small (BA24+)
    longLabel Average mCG (small smooth) in BA24 (NeuN+) samples
    type bigWig
    color 255,20,147
    maxHeightPixels 100:30:8

    track BA9_pos.small_smooth.mCG
    parent mCG on
    subGroups NeuN=A_pos Tissue=A_BA9 Smooth=A_small Comparison=F_NA view=A_mCG
    bigDataUrl BA9_pos.small_smooth.mCG.bw
    shortLabel mCG small (BA9+)
    longLabel Average mCG (small smooth) in BA9 (NeuN+) samples
    type bigWig
    color 0,191,255
    maxHeightPixels 100:30:8

    track HC_pos.small_smooth.mCG
    parent mCG off
    subGroups NeuN=A_pos Tissue=C_HC Smooth=A_small Comparison=F_NA view=A_mCG
    bigDataUrl HC_pos.small_smooth.mCG.bw
    shortLabel mCG small (HC+)
    longLabel Average mCG (small smooth) in HC (NeuN+) samples
    type bigWig
    color 169,169,169
    maxHeightPixels 100:30:8

    track NAcc_pos.small_smooth.mCG
    parent mCG on
    subGroups NeuN=A_pos Tissue=D_NAcc Smooth=A_small Comparison=F_NA view=A_mCG
    bigDataUrl NAcc_pos.small_smooth.mCG.bw
    shortLabel mCG small (NAcc+)
    longLabel Average mCG (small smooth) in NAcc (NeuN+) samples
    type bigWig
    color 255,127,36
    maxHeightPixels 100:30:8

    track BA24_neg.small_smooth.mCG
    parent mCG off
    subGroups NeuN=B_neg Tissue=B_BA24 Smooth=A_small Comparison=F_NA view=A_mCG
    bigDataUrl BA24_neg.small_smooth.mCG.bw
    shortLabel mCG small (BA24-)
    longLabel Average mCG (small smooth) in BA24 (NeuN-) samples
    type bigWig
    color 255,20,147
    maxHeightPixels 100:30:8

    track BA9_neg.small_smooth.mCG
    parent mCG off
    subGroups NeuN=B_neg Tissue=A_BA9 Smooth=A_small Comparison=F_NA view=A_mCG
    bigDataUrl BA9_neg.small_smooth.mCG.bw
    shortLabel mCG small (BA9-)
    longLabel Average mCG (small smooth) in BA9 (NeuN-) samples
    type bigWig
    color 0,191,255
    maxHeightPixels 100:30:8

    track HC_neg.small_smooth.mCG
    parent mCG off
    subGroups NeuN=B_neg Tissue=C_HC Smooth=A_small Comparison=F_NA view=A_mCG
    bigDataUrl HC_neg.small_smooth.mCG.bw
    shortLabel mCG small (HC-)
    longLabel Average mCG (small smooth) in HC (NeuN-) samples
    type bigWig
    color 169,169,169
    maxHeightPixels 100:30:8

    track NAcc_neg.small_smooth.mCG
    parent mCG off
    subGroups NeuN=B_neg Tissue=D_NAcc Smooth=A_small Comparison=F_NA view=A_mCG
    bigDataUrl NAcc_neg.small_smooth.mCG.bw
    shortLabel mCG small (NAcc-)
    longLabel Average mCG (small smooth) in NAcc (NeuN-) samples
    type bigWig
    color 255,127,36
    maxHeightPixels 100:30:8

    track BA24_unsorted.small_smooth.mCG
    parent mCG off
    subGroups NeuN=C_unsorted Tissue=B_BA24 Smooth=A_small Comparison=F_NA view=A_mCG
    bigDataUrl BA24_unsorted.small_smooth.mCG.bw
    shortLabel mCG small (BA24)
    longLabel Average mCG (small smooth) in BA24 (unsorted) samples
    type bigWig
    color 255,20,147
    maxHeightPixels 100:30:8

    track BA9_unsorted.small_smooth.mCG
    parent mCG off
    subGroups NeuN=C_unsorted Tissue=A_BA9 Smooth=A_small Comparison=F_NA view=A_mCG
    bigDataUrl BA9_unsorted.small_smooth.mCG.bw
    shortLabel mCG small (BA9)
    longLabel Average mCG (small smooth) in BA9 (unsorted) samples
    type bigWig
    color 0,191,255
    maxHeightPixels 100:30:8

    track HC_unsorted.small_smooth.mCG
    parent mCG off
    subGroups NeuN=C_unsorted Tissue=C_HC Smooth=A_small Comparison=F_NA view=A_mCG
    bigDataUrl HC_unsorted.small_smooth.mCG.bw
    shortLabel mCG small (HC)
    longLabel Average mCG (small smooth) in HC (unsorted) samples
    type bigWig
    color 169,169,169
    maxHeightPixels 100:30:8

    track NAcc_unsorted.small_smooth.mCG
    parent mCG off
    subGroups NeuN=C_unsorted Tissue=D_NAcc Smooth=A_small Comparison=F_NA view=A_mCG
    bigDataUrl NAcc_unsorted.small_smooth.mCG.bw
    shortLabel mCG small (NAcc)
    longLabel Average mCG (small smooth) in NAcc (unsorted) samples
    type bigWig
    color 255,127,36
    maxHeightPixels 100:30:8

    track BA24_pos.large_smooth.mCG
    parent mCG off
    subGroups NeuN=A_pos Tissue=B_BA24 Smooth=B_large Comparison=F_NA view=A_mCG
    bigDataUrl BA24_pos.large_smooth.mCG.bw
    shortLabel mCG large (BA24+)
    longLabel Average mCG (large smooth) in BA24 (NeuN+) samples
    type bigWig
    color 255,20,147
    maxHeightPixels 100:30:8

    track BA9_pos.large_smooth.mCG
    parent mCG off
    subGroups NeuN=A_pos Tissue=A_BA9 Smooth=B_large Comparison=F_NA view=A_mCG
    bigDataUrl BA9_pos.large_smooth.mCG.bw
    shortLabel mCG large (BA9+)
    longLabel Average mCG (large smooth) in BA9 (NeuN+) samples
    type bigWig
    color 0,191,255
    maxHeightPixels 100:30:8

    track HC_pos.large_smooth.mCG
    parent mCG off
    subGroups NeuN=A_pos Tissue=C_HC Smooth=B_large Comparison=F_NA view=A_mCG
    bigDataUrl HC_pos.large_smooth.mCG.bw
    shortLabel mCG large (HC+)
    longLabel Average mCG (large smooth) in HC (NeuN+) samples
    type bigWig
    color 169,169,169
    maxHeightPixels 100:30:8

    track NAcc_pos.large_smooth.mCG
    parent mCG off
    subGroups NeuN=A_pos Tissue=D_NAcc Smooth=B_large Comparison=F_NA view=A_mCG
    bigDataUrl NAcc_pos.large_smooth.mCG.bw
    shortLabel mCG large (NAcc+)
    longLabel Average mCG (large smooth) in NAcc (NeuN+) samples
    type bigWig
    color 255,127,36
    maxHeightPixels 100:30:8

    track BA24_neg.large_smooth.mCG
    parent mCG off
    subGroups NeuN=B_neg Tissue=B_BA24 Smooth=B_large Comparison=F_NA view=A_mCG
    bigDataUrl BA24_neg.large_smooth.mCG.bw
    shortLabel mCG large (BA24-)
    longLabel Average mCG (large smooth) in BA24 (NeuN-) samples
    type bigWig
    color 255,20,147
    maxHeightPixels 100:30:8

    track BA9_neg.large_smooth.mCG
    parent mCG off
    subGroups NeuN=B_neg Tissue=A_BA9 Smooth=B_large Comparison=F_NA view=A_mCG
    bigDataUrl BA9_neg.large_smooth.mCG.bw
    shortLabel mCG large (BA9-)
    longLabel Average mCG (large smooth) in BA9 (NeuN-) samples
    type bigWig
    color 0,191,255
    maxHeightPixels 100:30:8

    track HC_neg.large_smooth.mCG
    parent mCG off
    subGroups NeuN=B_neg Tissue=C_HC Smooth=B_large Comparison=F_NA view=A_mCG
    bigDataUrl HC_neg.large_smooth.mCG.bw
    shortLabel mCG large (HC-)
    longLabel Average mCG (large smooth) in HC (NeuN-) samples
    type bigWig
    color 169,169,169
    maxHeightPixels 100:30:8

    track NAcc_neg.large_smooth.mCG
    parent mCG off
    subGroups NeuN=B_neg Tissue=D_NAcc Smooth=B_large Comparison=F_NA view=A_mCG
    bigDataUrl NAcc_neg.large_smooth.mCG.bw
    shortLabel mCG large (NAcc-)
    longLabel Average mCG (large smooth) in NAcc (NeuN-) samples
    type bigWig
    color 255,127,36
    maxHeightPixels 100:30:8

### ============================================================================
### mCA
###

track WGBS_mCA
compositeTrack on
visibility full
# NOTE: "[A-Z]_" prefix on subGroup tags is to manually set sortOrder
subGroup1 view Views \
  A_mCA=mCA \
  B_CA-DMR=Differentially_methylated_regions
subGroup2 NeuN NeuN_status \
  A_pos=NeuN+ \
  B_neg=NeuN- \
  C_unsorted=Unsorted \
  D_union=Union \
  E_NA=Not_applicable
subGroup3 Tissue Brain_region \
  A_BA9=Dorsolateral_prefrontal_cortex \
  B_BA24=Anterior_cingulate_gyrus \
  C_HC=Hippocampus \
  D_NAcc=Nucleus_accumbens \
  E_union=Union \
  F_NA=Not_applicable
subGroup4 Comparison Comparison \
  A_pos=Between_brain_regions_in_NeuN+_samples \
  B_neg=Between_brain_regions_in_NeuN-_samples \
  C_pos_vs_neg=Between_NeuN+_and_NeuN-_samples \
  D_NAcc_pos_vs_BA9_pos=Between_NAcc_(NeuN+)_and_BA9_(NeuN+)_samples \
  E_unsorted=Between_brain_regions_in_unsorted_samples \
  F_NA=Not_applicable
dimensions dimX=Tissue dimY=NeuN dimA=Comparison
filterComposite dimA
sortOrder NeuN=+ Tissue=+ Comparison=+ view=+
type bed 3
shortLabel WGBS (mCA)
longLabel Average mCA in each condition and CA-DMRs
priority 2
html docs/WGBS

  track CA-DMRs
  parent WGBS_mCA on
  shortLabel CA-DMRs
  longLabel Differentially methylated regions using CpAs (CA-DMRs)
  view B_CA-DMR
  visibility squish
  type bigBed
  viewUi on

    track CA_DMRs
    parent CA-DMRs on
    subGroups NeuN=A_pos Tissue=F_NA Comparison=A_pos view=B_CA-DMR
    bigDataUrl CA-DMRs.bb
    shortLabel CA-DMRs (+)
    longLabel CA-DMRs between brain regions in NeuN+ samples
    type bigBed 6
    colorByStrand 0,0,0 190,190,190
    priority 2

  track mCA
  parent WGBS_mCA on
  shortLabel mCA
  longLabel Average mCA in each condition
  view A_mCA
  visibility full
  type bigBed
  viewUi on
  # NOTE: viewLimits were chosen by trial and error. They happen to roughly
  #       coincide with the 0.99 quantile of mCA in BA9_pos
  viewLimits -0.25:0.25
  yLineOnOff on
  yLineMark 0
  gridDefault on

    track BA24_pos.mCA
    parent mCA off
    subGroups NeuN=A_pos Tissue=B_BA24 Comparison=F_NA view=A_mCA
    bigDataUrl BA24_pos.mCA.bw
    shortLabel mCA (BA24+)
    longLabel Average mCA in BA24 (NeuN+) samples
    type bigWig
    color 255,20,147
    maxHeightPixels 100:30:8

    track BA9_pos.mCA
    parent mCA on
    subGroups NeuN=A_pos Tissue=A_BA9 Comparison=F_NA view=A_mCA
    bigDataUrl BA9_pos.mCA.bw
    shortLabel mCA (BA9+)
    longLabel Average mCA in BA9 (NeuN+) samples
    type bigWig
    color 0,191,255
    maxHeightPixels 100:30:8

    track HC_pos.mCA
    parent mCA off
    subGroups NeuN=A_pos Tissue=C_HC Comparison=F_NA view=A_mCA
    bigDataUrl HC_pos.mCA.bw
    shortLabel mCA (HC+)
    longLabel Average mCA in HC (NeuN+) samples
    type bigWig
    color 169,169,169
    maxHeightPixels 100:30:8

    track NAcc_pos.mCA
    parent mCA on
    subGroups NeuN=A_pos Tissue=D_NAcc Comparison=F_NA view=A_mCA
    bigDataUrl NAcc_pos.mCA.bw
    shortLabel mCA (NAcc+)
    longLabel Average mCA in NAcc (NeuN+) samples
    type bigWig
    color 255,127,36
    maxHeightPixels 100:30:8

### ============================================================================
### mCT
###

track WGBS_mCT
compositeTrack off
visibility hide
# NOTE: "[A-Z]_" prefix on subGroup tags is to manually set sortOrder
subGroup1 view Views \
  A_mCT=mCT \
  B_CT-DMR=Differentially_methylated_regions
subGroup2 NeuN NeuN_status \
  A_pos=NeuN+ \
  B_neg=NeuN- \
  C_unsorted=Unsorted \
  D_union=Union \
  E_NA=Not_applicable
subGroup3 Tissue Brain_region \
  A_BA9=Dorsolateral_prefrontal_cortex \
  B_BA24=Anterior_cingulate_gyrus \
  C_HC=Hippocampus \
  D_NAcc=Nucleus_accumbens \
  E_union=Union \
  F_NA=Not_applicable
subGroup4 Comparison Comparison \
  A_pos=Between_brain_regions_in_NeuN+_samples \
  B_neg=Between_brain_regions_in_NeuN-_samples \
  C_pos_vs_neg=Between_NeuN+_and_NeuN-_samples \
  D_NAcc_pos_vs_BA9_pos=Between_NAcc_(NeuN+)_and_BA9_(NeuN+)_samples \
  E_unsorted=Between_brain_regions_in_unsorted_samples \
  F_NA=Not_applicable
dimensions dimX=Tissue dimY=NeuN dimA=Comparison
filterComposite dimA
sortOrder NeuN=+ Tissue=+ Comparison=+ view=+
type bed 3
shortLabel WGBS (mCT)
longLabel Average mCT in each condition and CT-DMRs
priority 3
html docs/WGBS

  track CT-DMRs
  parent WGBS_mCT off
  shortLabel CT-DMRs
  longLabel Differentially methylated regions using CpTs (CT-DMRs)
  view B_CT-DMR
  visibility squish
  type bigBed
  viewUi on

    track CT_DMRs
    parent CT-DMRs off
    subGroups NeuN=A_pos Tissue=F_NA Comparison=A_pos view=B_CT-DMR
    bigDataUrl CT-DMRs.bb
    shortLabel CT-DMRs (+)
    longLabel CT-DMRs between brain regions in NeuN+ samples
    type bigBed 6
    colorByStrand 0,0,0 190,190,190
    priority 2

  track mCT
  parent WGBS_mCT off
  shortLabel mCT
  longLabel Average mCT in each condition
  view A_mCT
  visibility full
  type bigBed
  viewUi on
  # NOTE: viewLimits were chosen by trial and error. They happen to roughly
  #       coincide with the 0.99 quantile of mCA in BA9_pos. This is
  #       intentional to display mCA and mCT on the same scale.
  viewLimits -0.25:0.25
  yLineOnOff on
  yLineMark 0
  gridDefault on

    track BA24_pos.mCT
    parent mCT off
    subGroups NeuN=A_pos Tissue=B_BA24 Comparison=F_NA view=A_mCT
    bigDataUrl BA24_pos.mCT.bw
    shortLabel mCT (BA24+)
    longLabel Average mCT in BA24 (NeuN+) samples
    type bigWig
    color 255,20,147
    maxHeightPixels 100:30:8

    track BA9_pos.mCT
    parent mCT on
    subGroups NeuN=A_pos Tissue=A_BA9 Comparison=F_NA view=A_mCT
    bigDataUrl BA9_pos.mCT.bw
    shortLabel mCT (BA9+)
    longLabel Average mCT in BA9 (NeuN+) samples
    type bigWig
    color 0,191,255
    maxHeightPixels 100:30:8

    track HC_pos.mCT
    parent mCT off
    subGroups NeuN=A_pos Tissue=C_HC Comparison=F_NA view=A_mCT
    bigDataUrl HC_pos.mCT.bw
    shortLabel mCT (HC+)
    longLabel Average mCT in HC (NeuN+) samples
    type bigWig
    color 169,169,169
    maxHeightPixels 100:30:8

    track NAcc_pos.mCT
    parent mCT on
    subGroups NeuN=A_pos Tissue=D_NAcc Comparison=F_NA view=A_mCT
    bigDataUrl NAcc_pos.mCT.bw
    shortLabel mCT (NAcc+)
    longLabel Average mCT in NAcc (NeuN+) samples
    type bigWig
    color 255,127,36
    maxHeightPixels 100:30:8