Hello Anja, Unfortunately it is not possible to output the isPCR results within the browser in BED format. If you aren't doing very many queries you can take the coordinates that are output and convert them to BED format manually. You can read more about BED format in this FAQ:
http://genome.ucsc.edu/FAQ/FAQformat.html#format1 If you have quite a few queries you may be interested in our command line utility isPcr that does the same thing as the isPCR cgi (http://genome.ucsc.edu/cgi-bin/hgPcr) within the browser. Please see this previously answered mailing list question: https://lists.soe.ucsc.edu/pipermail/genome/2011-February/025080.html You can read more about downloading and using our source code here: http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads if you run the isPcr tool with the -out=bed flag you should be able to get BED format output and if you run it with no arguments you can see the usage statement for more detail on all the options. For BLAT, you can choose output type "psl" and make a custom track and output that from the table browser in BED format. For more details on that process please see this previously answered mailing list question: https://lists.soe.ucsc.edu/pipermail/genome/2012-March/028712.html Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 3/21/12 4:41 PM, Anja Rockstroh wrote: > Dear UCSC team, > > I am frequently using the in-silico PCR and BLAST tools and was wondering > whether there is a way to retrieve the information from those newly created > tracks in BED format? I have tried using the Table Browser, but the PCR and > BLAST tracks are not listed in the "track" drop down menu. > > Thanks very much, > Anja > > Anja Rockstroh | Research Fellow | Australian Prostate Cancer Research Centre > - Queensland | Institute of Health and Biomedical Innovation | Queensland > University of Technology > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
