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 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,
UCSC Genome Bioinformatics Group