Hi Jia, pslMap is a command-line tool that is available as part of the Genome Browser source tree (which is free for academic, non-profit and personal use). To download the source tree, go to the link provided, http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads, and click on the first link, "UCSC Genome Browser source download." Follow the build instructions on our website to build and install the source (http://genome.ucsc.edu/admin/jk-install.html).
Once you download the source tree and build it, you can run the command with no arguments to get a usage statement. Also see kent/src/hg/pslMap/README for more information about using pslMap. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 8/5/11 12:43 PM, Zeng, Jia wrote: > To whom it may concern: > > I would like use the utility in UCSC to extract the orthologous region in > chimpanzee genome given a human genomic intervals, which are well annotated > generic region (based upon hg19). I have the start and end coordinates for > these region. I wonder if there is any good tools in UCSC I can use to search > in the chimpanzee genome > > Actually, I asked some experts in UCSC genome browser before. Here is her > response: > > "Note that you may also find the pslMap tool handy as it is actually > meant for lifting over items with finer structure like genes." > > She also give me this link to find the source code: > > http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads > > However, I search through the website but can't find any tool called > "pslMap". Could you provide me the exact link to this tool? Or you suggest > any other similar tools. > > Many thanks in advance! > > Best, > > Jia Zeng > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
