Sorry, my initial request was a bit muddled! I generally use the UCSC BLAT server to realign a small number of next-gen sequencing short reads. These reads overlap, and any mismatches are displayed by the UCSC browser as single white letters in a black bar representing the read. A heterozygous genotype in the input reads is easily apparent as a "mismatch" in about half the reads. Combined with a vaiety of other tracks in the browser, this provides a very nice view of the data at a given locus.
Due to the limit on 25 reads, this approach is often not very useful. I have been running BLAT locally on hundreds on short reads, and am now trying to upload this BLAT output to the UCSC genome browser, and have it display the same as output from the UCSC BLAT server is displayed. The best I can do is use a modified MAF file, in which mismatches are shown as a letter, and bases the same as reference are displayed as a dot. While this works, the output would be much more visually appealing if I could adjust some settings to display the reads as black bars, with white letters illustrating the mismatches. I have looked at the UCSC browser source code (thanks for making it available!!), but I can't figure out a way to use your settings for a custom track. Maybe it isn't possible, but any insight would be appreciated! I've looked at the BLAT and custom track FAQs, and they weren't able to help. Thanks for your help! Jamie On 2/20/09 6:45 PM, "Jennifer Jackson" <[email protected]> wrote: > 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 >> -- Jamie K. Teer National Human Genome Research Institute National Institutes of Health phone: (301) 451-0252 fax: (301) 435-6170 _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
