Hello Vince, There is still not a way to get the Short Match track into a custom track (or some other text format) via the Genome Browser or the Table Browser.
There is a command-line tool called findMotif in the source tree that you could use. The source can be obtained from: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip Instructions for building the source: http://genome.ucsc.edu/admin/jk-install.html (note that you would not need to do step 7) The program is located in src/utils/findMotif/. Run it without arguments to get this usage statement: $ findMotif findMotif - find specified motif in sequence usage: findMotif [options] -motif=<acgt...> sequence where: sequence is a .fa , .nib or .2bit file or a file which is a list of sequence files. options: -motif=<acgt...> - search for this specified motif (case ignored, [acgt] only) -chr=<chrN> - process only this one chrN from the sequence -strand=<+|-> - limit to only one strand. Default is both. -bedOutput - output bed format (this is the default) -wigOutput - output wiggle data format instead of bed file -verbose=N - set information level [1-4] NOTE: motif must be longer than 4 characters, less than 17 -verbose=4 - will display gaps as bed file data lines to stderr If you have further questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 03/13/11 12:19, Vince Forgetta wrote: > Hi, > > Is there a method to obtain the short match track in bed format? > > I found this thread from 2008: > > https://lists.soe.ucsc.edu/pipermail/genome/2008-August/016939.html > > Has any progress been made? > > Can you think of a "hack" to get this data e.g. using a custom SQL query via > the table browser? > > Thanks. > > Vince > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
