Hi Jeremy, If you are running a mirror of our genome browser, then you should be able to create such a track. If that's the case, let us know and we can give you more detailed instruction. Here's the information about creating a mirror: http://genome.ucsc.edu/admin/mirror.html
The Genome Browser and Blat software are free for academic, nonprofit, and personal use. A license is required for commercial use. If you are, instead, trying to do this using our website and source code tools, I cam give you some pointers to get that done. You will use two kent source tools: pslPretty and axtToMaf. In general (for PSL -> MAF translation): pslPretty -axt | axtToMaf See this previously-answered mail list question for more details: http://www.soe.ucsc.edu/pipermail/genome/2008-November/017574.html You may have to make a few edits to the resulting MAF file in order to display it as a Custom Track. Read more about creating a MAF Custom Track here: http://genome.ucsc.edu/FAQ/FAQformat.html#format5 I hope this information is helpful to you. Please don't hesitate to contact the mail list again if you require further assistance. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu Jeremy Davis-Turak wrote: > Hi, > > I'm trying to create a track of aligned Illumina sequencing reads. > Currently I am using a .BED file, but I am having trouble with > displaying the mismatches in those alignments. I would like to have > them look just like the BLAT alignment results, where mismatches have > a changed base, and indels are shown. However, the PSLX format does > not seem to be supported. I noticed that the BLAT results are a > combination of a .FA file and and a .PSL file. Is there any support > for creating combining these files, outside of using BLAT? > > Thanks, > > Jeremy > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
