Hi Yishay, You will not be able to retrieve this information from the Table Browser. One of our engineers suggests you try pslMap. 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). Download the source tree from here: 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 view the usage statement. Also see kent/src/hg/pslMap/README for more information about using pslMap.
You can use refSeqAli table and convert this table into a PSL of transcripts using the following Linux command "cut -f 2-22". You will also have to create a BED file (see http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED) containing your data, for example: NM_053102 844 845 NM_053102:845 Note that chromStart is one less than chromEnd, this is because the representations of coordinates always have a zero-based start and one-based end (see http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1). Then, you will have to convert the 4-field BED representation to a "fake" PSL like this: cut -f 10,11 mm9.refSeqAli.psl> mm9.refSeq.sizes bedToPsl mm9.refSeq.sizes test.bed test.in.psl Run pslMap: pslMap test.in.psl mm9.refSeqAli.psl test.out.psl pslToBed test.out.psl stdout | cut -f 1-4> test.out.bed You should get the following output: chr3 144259975 144259976 NM_053102:845 For more information on PSL, please see: http://genome.ucsc.edu/goldenPath/help/customTrack.html#PSL. I hope this helps. Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 10/9/2011 4:46 AM, yishay pinto wrote: > Hello, > I have refseq ID and location, for example:NM_053102 location:845 and I want > to convert it to genomic coordinate like: chrX, 50374459, + . > is there any possible way to so that? I tried with the table browser but i > did not succeed to give him specific location on the refseq id. > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
