Invalid: 'type = lines' When I want to plot the result of TAD.

[XinmingTu]

I just follow the "Hi-C analysis of mouse ESCs using HiCExplorer" but when I try to use

I just get this.

so I delete the "type = lines", then try again, this time I got a pdf, but there is not TAD, it's just like this

So how can I get a right pdf?

[XinmingTu]

My track.ini is

I think there is no mistake.

[joachimwolff]

Hi,

you use the beta version of release 2.2, but the documentation is for the stable version 2.1.4 and not updated to 2.2 so far.

Things you can do:

• Downgrade to stable version 2.1.4
• Stay at 2.2beta version and change in the init file the [hic] section to:

[hic]
file = hicMatrix/replicateMerged.Corrected_20kb.h5
title = your title
colormap = RdYlBu_r
depth = 2000000
transform = log1p
x labels = yes
file_type = hic_matrix
height = 5

[tads]
file = domains.bed
file_type = domains
border color = black
color = none
height = 5
line width = 1.5
overlay previous = share-y
show data range = no

Please replace width with height in all your tracks.

Best,

Joachim

[XinmingTu]

Yeah! Thank you, I got the TADs on the pdf, but it's not what I want.

[hic]
file = hicMatrix/replicateMerged.Corrected_20kb.h5
title = Hic mESC chrX:99974316-101359967
colormap = RdYlBu_r
depth = 2000000
transform = log1p
x labels = yes
file_type = hic_matrix
height = 5

[x-axis]
fontsize=16
where=top

[tads]
file = TADs/marks_et-al_TADs_20kb-Bins_score.bedgraph
file_type = bedgraph
border color = black
color = none
height = 5
line width = 1.5
overlay previous = share-y
show data range = no

[tad score]
file = TADs/marks_et-al_TADs_20kb-Bins_score.bedgraph
title = "TAD separation score"
height  = 2
line_width = 1.5
color = blue
file_type = bedgraph

[spacer]

[gene track]
file = mm10_genes_sorted.bed
width = 10
title = "mm10 genes"
width = 5
labels = off

• If I want to plot the TADs on the matrix, What should I do? As for downgrade to stable version 2.1.4, I try

  conda install HiCExplorer-2.1.4

  but it failed.

• If I want to plot the data, the plotHic section in documentation is for 2.2 ？

Thank you again. Best, Xinming

[joachimwolff]

Hi Xinming,

to install it via conda use: conda install hicexplorer=2.1.4

The documentation is for 2.1.4 only, we work atm on the updated version for 2.2.

Best,

Joachim

[XinmingTu]

Thank you so much!! Looking forward the new documentation!