3D chromatin structures of human embryos#

Hi-C data from this study:

Chen X, Ke Y, Wu K, et al. Key role for CTCF in establishing chromatin structure in human embryos[J]. Nature, 2019, 576(7786): 306-310.

origin image

image098.png

CLI mode#

conf-embryos.yml

trackc:
  - ax: t1
    height: 1
    track_type: hicmap
    track_para:
      mat:
        method: extractCisContact
        clr: h2cell.mcool::/resolutions/100000
        extend: 50
      mapC:
        map_type: rec
        height: 50
        label: 2-cell
        cmap: PuBu
  - ax: t2
    height: 1
    track_type: hicmap
    track_para:
      mat:
        method: extractCisContact
        clr: h8cell.mcool::/resolutions/100000
        extend: 50
      mapC:
        map_type: rec
        height: 50
        label: 8-cell
        cmap: PuBu
  - ax: t3
    height: 1
    track_type: hicmap
    track_para:
      mat:
        method: extractCisContact
        clr: morula.mcool::/resolutions/100000
        extend: 50
      mapC:
        map_type: rec
        height: 50
        label: Morula
        cmap: PuBu
  - ax: t4
    height: 1
    track_type: hicmap
    track_para:
      mat:
        method: extractCisContact
        clr: blastocyst.mcool::/resolutions/100000
        extend: 50
      mapC:
        map_type: rec
        height: 50
        label: Blastocyst
        cmap: PuBu
  - ax: t5
    height: 1
    track_type: hicmap
    track_para:
      mat:
        method: extractCisContact
        clr: h6week.mcool::/resolutions/100000
        extend: 50
      mapC:
        map_type: rec
        height: 50
        label: 6-week
        cmap: PuBu
  - ax: t6
    height: 1
    track_type: hicmap
    track_para:
      mat:
        method: extractCisContact
        clr: H1ESC.mcool::/resolutions/100000
        extend: 50
      mapC:
        map_type: rec
        height: 50
        label: H1 hESC
        cmap: PuBu
  - ax: t1
    track_type: scale_track
    track_para:
      scale_adjust: Mb
      tick_pos: top
      ratio2ax: 1

trackc cli conf-embryos.yml -r chr7:17000000-28940000 -o test3.pdf

qwerui