How to obtain tracks?

[Bryant, William01]

Dear UCSC Genome Browser,

I am using CLC Genomics Workbench which has overlaying tracks (genome, mRNA and expression from RNA-Seq data). However, I want to be able to download and import tracks from UCSC into CLC as a means to combine CLC capabilities with UCSC. 

Where in the UCSC website can I download GTF, Wiggle, or BED files for H3K4me3 as well as other tracks.

Thanks in advance,

Bart

W. B. Bryant Ph.D.

MIANO LAB

Augusta University

[Matthew Speir]

Hello, Bart.

Thank you for your question about accessing UCSC Genome Browser tracks.

All of our track data can be found on our download server: http://hgdownload.soe.ucsc.edu/downloads.html. Find your organism in the list at the top of the page and then click the link to be taken to a section of the page for that organism with subsections for each assembly and links to download different types of data. Tracks that are table based end up under the link "Annotations > SQL table dump annotations". Tracks based on our "big" file types (e.g. bigWig or bigBed) can be found under "Annotations > Fileserver (bigBed, maf, fa, etc) annotations". You can use our video, https://www.youtube.com/watch?v=RQZ4EeYS6Zk, to find out how to find the name used for the files or tables.

For gene tracks (e.g. NCBI RefSeq, etc.), we do provide GTF files. You can find those under the "Genome sequence files and select annotations (2bit, GTF, GC-content, etc)" link for each assembly.

Lastly, you can use our "Track Search" tool to find tracks, such as those covering H3K4me3 marks. After selecting your assembly on our Gateway page, http://genome.ucsc.edu/cgi-bin/hgGateway, you can use the "Track Search" tool in the drop-down menu under "Genome Browser" in the top menu.

I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Training videos & resources: http://genome.ucsc.edu/training/index.html

Want to share the Browser with colleagues? Host a workshop: http://bit.ly/ucscTraining

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Matthew Speir

UCSC Cell Browser, Quality Assurance and Data Wrangler

Human Cell Atlas, User Experience Researcher

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.

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