Question about downloading ChromHMM .bed data
Gong, Yixiao
Howard Hughes Medical Institute
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Brian Lee
Dear Yixiao Gong,
Thank you for using the UCSC Genome Browser and your question about accessing data for the Roadmap ChromHMM Core Marks Track of the Roadmap Epigenomics Data hub.
This data is from a Public Hub that is hosted by WashU, http://vizhub.wustl.edu/, and the listed contact for the hub is tw...@genetics.wustl.edu. It is likely best to contact them directly to find the best way to access their data.
To access the files you are seeing displayed in the browser, you can navigate their public hub's directories and find the trackDb file that points via "bigDataUrl" statements to the location of each file displayed. Below are some short scripts you can put on the command line that will pull out those statements and create links via the relative location of the defined files. First obtains the URLs of all the files, followed by just the .bigBed and .bb files, however, not filtered for only the ChromHMM track.
curl -silent http://vizhub.wustl.edu/VizHub/hg19/trackDb_dli_edacc8_new4.txt | grep bigDataUrl | sed -e 's#^.*bigDataUrl #http://vizhub.wustl.edu/VizHub/hg19/#' curl -silent http://vizhub.wustl.edu/VizHub/hg19/trackDb_dli_edacc8_new4.txt | grep bigDataUrl | sed -e 's#^.*bigDataUrl #http://vizhub.wustl.edu/VizHub/hg19/#' | grep 'bb\|bigBed'
These are the binary bigBed files that can be turned into bed files with the bigBedToBed utility located in the appropriate directory here: http://hgdownload.soe.ucsc.edu/admin/exe/
Another approach is to use our Table Browser. With the hub data displayed in the browser, click the top "Tools" button and navigate to the Table Browser and then set the group to "Roadmap Epigenomics Data Complete Collection at Wash U VizHub" and then select the "Roadmap ChromHMM" track at the very bottom of tracks. You could then choose each table and get the output from each track individually as bed files.
I suggest investigating the resources for accessing this externally hosted data (Public Track Hubs are not created or maintained by UCSC). You may also be interested in these tutorials about accessing Roadmap Epigenomics Data: http://www.genome.gov/27555330
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
Brian Lee
UCSC Genome Bioinformatics Group
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Daofeng Li
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Gong, Yixiao
Howard Hughes Medical Institute
Steve Heitner
Hello, Yixiao.
The “compositeTrack” label in the second line of the stanza indicates that “RoadmapHMM15” is actually a container for subtracks. The subtracks contain data, but the container does not, so there would be no bigDataUrl associated with the container.
Please contact us again at gen...@soe.ucsc.edu if you have any further questions. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Steve Heitner
UCSC Genome Bioinformatics Group
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