Download short match track as bed file?

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Froberg, John

Jun 17, 2014, 11:07:44 AM6/17/14

I am interested in downloading the output of the Short Match tool run for a short sequence against mm9 as a bedfile, which will provide a list of all instances of the motif of interest in the mm9 genome assembly. Is there any way to download the output of the Short Match tool as a bedfile? One previous answer to a similar question (!searchin/genome/short$20match/genome/85TponZ_RjM/7EJI3qg-Xc4J) suggested downloading the findMotif tool to obtain this information, and an early answer (!searchin/genome/short$20match/genome/rf7PJNcIjyg/ntq3-Je3SQoJ) implied that there is a way to download Short Match alignment coordinates from the browser, however that response links to a third response which appears to have been deleted. 

So has there been any progress obtaining Short Match alignment coordinates from the browser, without downloading and running findMotif?

Thank you very much,

John Froberg
Graduate Student, Lee Lab
Harvard University

Brian Lee

Jun 17, 2014, 12:59:32 PM6/17/14
to Froberg, John,
Dear John,

Thank you for using the UCSC Genome Browser and your question about downloading the short match track as a bed file.

The current path available will require running a command line utility, such as tacg or findMotif.

If you wish to use our findMotif utility, you can download it from here:

For example, if you are working in a macOSX.x86_64 environment:

Step1:   Download the appropriate utility for your environment
Step2: Make it executable 
chmod +x findMotif
Step3:  Run it on a 2bit file for a sequence, such as "aagaca":
./findMotif -motif=aagaca /path/to/a/sequenceSuchAS.GL339449.2bit

Get results in a bed format:
GL339449.1 938 944 1 1000 -
GL339449.1 2249 2255 2 1000 +

You can obtain the hg19.2bit file with the following command:

You may want to read more about the findMotif utility in our mailing list archives.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to 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

All the best,

Brian Lee
UCSC Genome Bioinformatics Group


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