Hi Anatole, Yes, this is the right place to ask questions about using the Genome Browser.
You will first want to create a custom track of your genomic locations. Then you can choose a gene track that suits your needs and intersect it with your custom track so that you only see the regions you are interested in. To create a custom track, put your positions in BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 (note that the start position should be one base less than normal), and then hit the "add custom tracks" button on the Genome Browser and either paste or upload the positions. To decide on the gene track you would like to use, go to the "Genes and Gene Prediction Tracks" section on http://genome.ucsc.edu/cgi-bin/hgTracks and click on the blue track names to read about how each was created (some are hand-curated, some are more inclusive than others, etc.). If you know you are going to need clusters of isoforms and one representative isoform for each cluster, you might want to use the "UCSC Genes" track, as the track has associated "knownIsoforms" and "knownCanonical" tables that might be useful. Once these two steps are done, go to the Table Browser and select the gene track. Hit the "intersection: create" button and intersect with your custom track. The results will be all of the genes from the track you chose that correspond to your genomic regions of interest. You can choose to get the output as a file or a custom track (or both). I hope this helps! If you have further questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/06/10 11:27, anatole ghazalpour wrote: > Hi, > > I hope I am emailing this to the correct email address. My name is Anatole and I am a research associate at UCLA. What I was interested to know was how do I find download isoforms of genes for a set of genomic locations. My data is made out of series of genomic locations which I have obtained by mapping my proteomic data to the genome. What I wanted to do is to see what isoforms of what genes these genomic locations represent. Is there any way I could do this using the table browser (or any other tool)? > > best, > > > Anatole > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
