Hello Jamie, The output on our server is a combination of file format input and the cgi./html that creates the browser page.
There may be something in the Blat FAQ to help? http://genome.ucsc.edu/FAQ/FAQblat.html Or better yet, the web Blat instructions on this page: http://genome.ucsc.edu/goldenPath/help/blatSpec.html If you still need technical help after ready about the web Blat, please write back and let us know, Jennifer Jackson UCSC Genome Bioinformatics Group Jamie Teer wrote: > I am trying to mimic the visual output of BLAT output from the UCSC BLAT > server. Specifically, I want to see black bars, with letter highlighting > variations in the sequence (what one would see after clicking on "browser" > in the BLAT output window.) I am trying to run BLAT locally, to get past > the 25 sequence limitation. I have searched the mailing list, and have > tried the pslPretty -axt | axtToMaf scripts, but do not get the same black > bar output with the differing bases being the only visible bases. I feel > that I might be misunderstanding the final modification needed in the maf > file itself. Can you go through the process in a bit more detail? Thanks! > Jamie > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
