To make a custom track directly from BLAT, select the PSL format output option. The resulting PSL track can be uploaded into the Genome Browser by pasting the data into the data text box on the Genome Browser Add Custom Tracks page, accessed via the "add custom tracks" button on the Browser gateway and annotation tracks pages. See the Creating custom annotation tracks section for more information.
For large batch jobs or internal parameter changes, it is best to install command line BLAT on your own Linux server. Sources and executables are free for academic, personal, and non-profit purposes. -BLAT source may be downloaded from http://www.soe.ucsc.edu/~kent (look for the blatSrc*.zip file with the +BLAT source may be downloaded from https://genome-test.gi.ucsc.edu/~kent/src/ +(look for the blatSrc*.zip file with the most recent date). For BLAT executables, go to http://genome-test.soe.ucsc.edu/~kent/exe/; binaries are sorted by platform. Non-exclusive commercial licenses are available from the Kent Informatics website.
For more information on the BLAT suite of programs, see the BLAT Program Specifications and the Blat section of the Genome Browser FAQ.
Detailed information about an individual annotation track, including display characteristics,