How to download track data from ucsc browser?

[Taxin, Zachary H (BIDMC - Endocrinology a Bone-Mineral)]

Hello,

 

I have searched high and low thru the forums and FAQs on UCSC and google for an answer to this question, and could not find one – therefore I am emailing.  I used both emails because I am honestly not sure where this question falls.

 

Here is my problem: I am looking at tissue level differences in acetylation and methylation for a region of interest.  I have generated a file of hundreds of bigwig files from ENCODE and uploaded these to the custom tracks successfully.  I would like to download the track-level information (i.e. track signal peaks) for the specific DNA sequence in question (roughly 20kbp).  This way I can compare the signal intensity directly in a graphical form in aggregate between samples, for publication.  As it is, I can’t take screenshots of the data because 1) this is not reproducible, and 2) it does not demonstrate clearly the tissue level differences between samples (because there are too many tracks and the resolution would not be adequate).

 

Please let me know if there is any way to do this i.e. download custom track signal intensities for a specific region of DNA in the viewing window of the browser.

 

Thanks very much,

 

Zach Taxin

[Gerardo Perez]

Hello, Zach.

Thank you for your interest in the Genome Browser and your question about downloading track data in a specific region.

Unfortunately, we do not have a feature or a setting that downloads the data for all tracks in a specific region. We have created an internal ticket to add this as a feature, but we cannot provide a precise timeline for when it would be released.

One of our engineers shared that you could write a script to generate a file with a series of the bigWigToBedGraph utility and the -chrom=... -start=... -end=... commands to download the data for a specific region. You can download the bigWigToBedGraph utility from the downloads page, https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads. You can then find bigWigToBedGraph under the directory that matches your operating system. For example, here is the direct link for Linux:
http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph

You can run the utility on its own to see a help message, e.x.

$ ./bigWigToBedGraph
bigWigToBedGraph - Convert from bigWig to bedGraph format.
usage:
   bigWigToBedGraph in.bigWig out.bedGraph
options:
   -chrom=chr1 - if set restrict output to given chromosome
   -start=N - if set, restrict output to only that over start
   -end=N - if set, restict output to only that under end
   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs

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.

Gerardo Perez
UCSC Genomics Institute

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[Taxin, Zachary H (BIDMC - Endocrinology a Bone-Mineral)]

Thank you, this is quite helpful.  I will see if I can manage this.

Zach