Hello Louise, To determine this, you will need to compare genomic coordinates with an annotation track that you think is representative of the transcriptome. You may wish to combine two or more tracks to be inclusive or use a track with well characterized genes to be conservative (such as UCSC Genes). You did not mention whether you wish to distinguish between coding and non-coding exon regions - if this is important, stick with tracks with base tables of format genePred. If not, then many tracks from either the Gene Prediction or mRNA and EST groups could be candidates for your analysis. Click on the track description page to view details about what data is contained per track.
The next step is to get the coordinates into a BED format for these target track(s). Target track example: If you select the UCSC Genes track as your transcriptome, go the the Table browser, set the variables all the way down to the primary table: clade, genome, assembly, track group, track, and table = knownGene. Set region to genome. Set output as BED and submit. This will take you to a page where you can specify which regions should be in the output (exon, intron, coding, UTR, etc). It may take a few rounds to get all the data points. From here you can save as custom tracks to do the analysis in the Table browser and Galaxy Tool or download and perform the interval comparisons using your own tools. To stay using the Browser: Query track creation: Create a BED formatted file of your coordinates and upload as a custom track. Back in the Table Browser, send all of the query and target custom tracks to Galaxy (this is an output option). Once there, the data will be recognized as format "interval" or you will need to name them as interval. Here you can also merge all of your targets together into one file if desired. Then use the interval comparison tools to create the data merge. If your target was set up to include just exon/intron, then any position without a merge would be intergenic. Help links: http://genome.ucsc.edu/cgi-bin/hgTables http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html http://genome.ucsc.edu/FAQ/FAQformat We hope this helps to get you started, Jennifer Jackson UCSC Genome Bioinformatics Group Louise Laurent wrote: > Hi, > > I have a list of genomic positions (about 3000) that I'd like to check to > see if they are exonic, intronic, or intergenic. Is there a way to do this > in a batch? > > Thanks, > Louise > _______________________________________________ > Genome maillist - Genome@soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - Genome@soe.ucsc.edu http://www.soe.ucsc.edu/mailman/listinfo/genome
