Hello, This exact output is not available from the Table browser, however there are some options we can share to help.
You may want to try using an output format such as GTF for exons: http://genome.ucsc.edu/FAQ/FAQformat.html#format4 To only output one transcript per gene, filter using the knownCanonical table. This table contains the "representative" transcript for the gene, often the longest or most complete. Then merge these data with the UCSC Gene track's primary table linked with the HUGO Id as you already have done. Use your own tools or send the output over to Galaxy and try their utilities under the section "Text Manipulation" to start with (others may also be helpful). Thank you, Jennifer http://genome.ucsc.edu/cgi-bin/hgTables http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/12/10 8:01 AM, Christopher Watson wrote: > Hi, > I am trying to look up all exon co-ordinates for a number of different human > (Hg18) genes using the UCSC table browser. I can identify the gene > co-ordinates using the HUGO gene name in the table browser lookup box however > I am having trouble retrieving the appropriate exon data/format. > > I have been using the knownGene track in 'Genes and Gene Prediction Tracks> > UCSC Genes' as this contains the exon start / stop positions. I'm trying to > output each 'exon' with its start and stop positions on a separate line. At > the moment I can only output the data as a list of start and stop positions. > Also, I would like to include all the exons for a defined gene without > repetition, i.e. I would like the data to be transcript independent. For > example MYH7 has 39 and 40 exon entries but I would just like to see all 40 > exons in my output. If it is possible to include the HUGO gene name field > this would also be incredibly useful to me. > > Could anyone let me know how this can best be achieved? I have ~60 genes for > which I need to generate this data. > > Regards, Christopher Watson. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
