Hi All
First, thank you very much for creating a web based tool so we can visualize our tracks on it. It is awesome.
However, I have been struggling to visualize my data.
I have followed the suggestions on installing Hicbrowser and editing the config file but it is not working properly.
I am using an ubuntu operating system and google chrome to visualize the example tracks such as H3K36me3.bw and H3K27me3.bw from modendcode.
The tracks are loading but they are cutting off and the visualization is not useful after they load. I will be very grateful for your concern if you guys can kindly point me the errors in my file and show me the right way to edit the config file. I am very new to this.

Here are the details of my config files:

filename: browserConfig.ini

[general]
tracks= gene_tracks.ini
TAD intervals= domains.bed
genes= dm3_genes.bed.gz

[browser]
tracks=tracks.ini

filename: gene_tracks.ini

[TADs]
file = _domains.bed
title = peaks
color = red
width = 3
file_type = boundaries

[x-axis]
fontsize=10

[spacer]

[genes]
file = <my_genes>.bed
title = genes
color = darkblue
width = 15
labels = on
type = genes
file_type = bed
fontsize = 10

filename: tracks.ini

[hic]
file = Li_et_al_2015.h5
title = Li_et_al_2015
colormap = RdYlBu_r
depth = 100000
min_value =2.8
max_value = 3.0
file_type = hic_matrix
show_masked_bins = yes
scale factor = 1

[x-axis]
fontsize=20
where=top

[spacer]

[x-axis]
fontsize=10
where=top

[spacer]

[bigwig]
file = H3K36me3.bw
title = H3K36me3
color = black
width = 1.5
min_value = 0
max_value = auto
number of bins = 500
nans to zeros = True
type = points
show data range = yes
scale factor = 0.25
file_type = bigwig

[spacer]

[bigwig]
file = H3K27me3.bw
title = H3K27me3
color = red
width = 1.5
min_value = 0
max_value = auto
number of bins = 500
nans to zeros = True
type = points
show data range = yes
scale factor = 0.25
file_type = bigwig

Appreciate your help.

Thanking you
Rocky

Hello,

I was wondering if this is still supported or not. I have had issues installing and getting the browser running. the runBrowser command cannot find trackPlot.py in hicexplorer and indeed it does not exist there. Is there another way to use this program?

Thanks

Current config (.ini) file has it's own format, while yaml is a popular and easy to use format. Plus I am not sure if current config allows a hierarchy in the dictionary keys obtained after parsing. If we have a hierarchy of keys we can merge the gene config and browser config file into one and then we require only one config at browser startup.

For example:

gene_view:
    boundaries_bed:
        file: /path/to/file
        title: TADs
        color: red
    genes:
        file: /data/test/hicBrowser/GRCm38_genes2.bed 
        title: genes
        color: darkblue
region_view:
    hic_file:
        file: /data/test/hicBrowser/mF1216_merged_10k.h5 
        title: mF1216
        colormap: RdYlBu_r
        depth: 1000000
    bigwig:
        file: /data/test/hicBrowser/H3k4me3.bw 
        title: H3K4me3

HiCBrowser loads all tracks twice in the debug mode..

Hi,

I have a query that I am having 2 samples (control.cool and treatment.cool) and ran hicCompareMatrix command and obtained a combined matrix file (combine.cool) and then used hiCPlotMatrix to plot this cool file with coordinates range like 8000000-9000000 and one plot with range 3000000-4000000. I have 80 coordinates like this and now I want to have a plot averaging 80 coordinates.

can anyone please help me in this.

By chance "image not found" appears. Sliding the window slightly mostly helps...

The landing page of HiCBrowser says Drosophila chorogenome navigator.. We have to change it to something neutral (like the obvious : "HiCBrowser" or something..)

On the same issue : we need to create another landing page for the in-house hosted HiCBrowser instance...

HiCBrowser throws too many messages while loading.

Name of all genes.
All messages from HicExplorer
Name of all tracks TWICE..
Loading saving messages..

I propose removing everything, except name of all tracks (once) and loading/saving messages..

If we want to reuse a container for multiple genomes and datatsets we need to encode the example regions and genes in dynamic way.

Hi,
I would be interested to use HiCBrowser but get this error:

pip install git+git//github.com/maxplanck-ie/HiCBrowse@master

Invalid requirement: 'git+git//github.com/maxplanck-ie/HiCBrowse@master'
It looks like a path. File 'git+git//github.com/maxplanck-ie/HiCBrowse@master' does not exist.

Atleast in the browsers fired by me (all different config files) .. Nothing happens when i search by genes..

Hello,

I have two problems with HiCBrowser and the runBrowser command.

• First, the gene search panel is not working, although the browserConfig.ini is pointing to a bed file working as intended as a [gene] track. The gene names are displayed in the browser, but when searching for the name of one of these genes, I get the following error:

Your search - FBtr0114187 - did not match any gene. Check the browser for examples of valid gene names as they may be an id.

While the genes= file.bed in browserConfig.ini has that specific line:
211000022278158 591 1036 FBtr0114187 0 + 1036 1036 0 1 445, 0,

• Second, the loading of [simple bed] data is failing, as I have Image Not Found displayed in the browser, although the bed file is ok and the chromosome names are corresponding to the other files. Here's the example of a [simple bed] object that fails to load in the regions_tracks.ini:

[simple bed]
file = /home/richard/Claudia/HAS/dm6_genes.bed
title = HAS
color = black
# optional boder color. Set to none for no border color
#border_color = black
width = 10
# optional. If not given is guessed from the file ending
file_type = bed

Ask you me if you need the browserConfig.ini, region_tracks.ini and the corresponding bed files.

Ping @gtrichard I moved your issue because it was posted in the wrong repository.

Orginal posting: deeptools/HiCExplorer#176

apart from the config file for the gene view and region view, there is no need for a third config file. HiCBrowser should directly be run with these two config files..

Hi,

I am trying to run HiCBrowser but keep getting this error message:

• Serving Flask app "hicbrowser.views" (lazy loading)

• Environment: production
  WARNING: Do not use the development server in a production environment.
  Use a production WSGI server instead.

• Debug mode: off

  raise ValueError("cannot have a multithreaded and "
  ValueError: cannot have a multithreaded and multi process server.

I am not sure whether this is due to the port number used.
I was wondering if anyone already experienced this and was able to resolve it?

The command I have been running is the following:

runBrowser --config browserConfig.ini --port 5001 --numProcessors 8
runBrowser --config browserConfig.ini --port 8888 --numProcessors 8

FYI, I am using a cluster to run this command.

Hi,
I would like to plot links for chomatin loop. How can I write region_tracks.ini file?

depending on the number of genes in the selected genic region the gene annotation track is either clipped or the genes are displayed at very large scale.
Would a dynamic scaling be possible (track height defined by number of overlapping genes).