Upload ChromHMM local track

[JUAN ANTONIO RODRIGUEZ]

Dear Dr. Li,

I am trying to visualize a simple chromhmm output file in your WashUBrowser, but I can't manage to get it working correctly. Following the docs, this is what I've done:

- From the output of ChromHMM I generated a bed file with chr, start, end, category state (sample txt attached):

- I compress it with: bgzip -f test_ChromHMM ; tabix -p bed test_ChromHMM.gz

- Finally upload both bed & index selecting "categorical" from the Upload Local Track option.

When I see the output in the browser I see my file represented in there, but I can't see it coloured by state (See screenshot attached). All different chromatin states show the same blue colour.

Previously, I have been able to upload a longrange track, and a ChipSeq bigWig from ENCODE, but now I can't correctly visualize this ChromHMM file. Maybe should I also upload a hub.config.json file? I tried to do it using the template you provide in the Docs, but no success. :( In case this is the way to go, could you provide me with a template file hub.config.json adapted to my file? (I'm not familiar with json files...)

Any help would be appreciated. 

I find your browser very useful to represent the different types of data I need for my research, and lately I have been using it a lot. Congrats for the good work.

Thank you so much in advance!

Best,

Juan

[lid...@gmail.com]

Hi Juan,

Thank you so much for using the browser and let us know it helps your research, we are very glad to hear that :)

For your question, since you see the track is loaded with all blue blocks, which means the track file itself is correct.

I am sorry currently for the single upload we did miss the options to allow the users to customize the track, which i will try to add asap.

right now you will need to configure a hub.config.json file, and specify options in it, option details can be found at https://eg.readthedocs.io/en/latest/tracks.html#categorical

for example, you can specify your track option like this:

[

{
    "type": "categorical",
    "name": "ChromHMM",
    "filename": "test_ChromHMM.gz",
    "options": {
        "category": {
            "1": {"name": "Active TSS", "color": "#ff0000"},
            "2": {"name": "Flanking Active TSS", "color": "#ff4500"},
            "3": {"name": "Transcr at gene 5' and 3'", "color": "#32cd32"}
        }
    }
}

]

please refer to https://eg.readthedocs.io/en/latest/local.html#upload-files-or-a-folder-as-a-datahub for more instructions.

Feel free to let me know any further question.

Thank you again.