Hello Valeria, This query is non-trivial to perform. It may take some experimentation to obtain the exact desired results. There are two choices we can offer that use mostly web-based tools, but both require some work with your own tools or perhaps there are some file manipulation options using Galaxy that would be useful (the Table browser can send data there as an output option). Help links follow below.
#1 Using the Table browser and the RefSeq Genes track the transcript/gene can be found, but not the particular exon with overlap. You would need to extract the data from the table then perform a comparison with the transcript alignment exons/blocks using your own tools. Select the clade, genome, assembly, group (Gene and Gene predictions), track (RefSeq Genes), and leave the default table = refGene. Then for region, paste or upload coordinates using the "define ranges" button. For output, leave the default "all fields from selected table". The transcriptID is in the field "name" and gene name is in the field "name2". #2 Using the Table browser and the UCSC Genes or RefSeq Genes track converted to GTF format, the exon of the transcript can be found, but the geneID will need to be mapped separately using your own tools or possibly a tool in Galaxy. In the current Table browser GTF format, the information labeled as "gene_id" is really the transcript name (same as the information labeled as "transcript_id"). This means that the actual gene name needs to be mapped back in as a separate step when using this file format. Select the clade, genome, assembly, group (Gene and Gene predictions), track (UCSC Genes or RefSeq Genes), and leave the default table = knownGene or refGene. Leave region = genome. For output, use GTF format and name file for download. Then reload the data as a custom track after adding an appropriate track line (see help links). Next create a BED file using your coordinates and also load as a custom track. Send both files over to Galaxy and perform an interval intersection. Once complete, obtain a copy of either the kgAlias table (for UCSC Genes) or the refGene table (for RefSeq Genes). Use this table to map between transcript to gene for your results using your own tools or possibly a join in Galaxy. Help for Table browser: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Help for Custom tracks: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks Help for Data file types: http://genome.ucsc.edu/FAQ/FAQformat.html Help for Galaxy is best found from that team, see the links in the upper tools bar once inside the tool. They have online help plus email support for questions. If you have programming resource, all of the database tables are available as files and creating a script to extract the data or using our utilities for some steps would be possible. Download data: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download1 Source code (contains all utilities): http://genome.ucsc.edu/FAQ/FAQdownloads.html#download27 http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities Selected precompiled: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ Hopefully this helps to get your started. You question came through twice, so this reply will be for both versions. Very sorry for the inconvenience of not being able to offer a more direct route to the answer. Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/5/10 9:55 AM, Vasta, Valeria wrote: > Hello > > > > Is there a way to obtain the gene name and exon with a list of > coordinates such as: > > > > chr1:10193340-10193459 > > chr1:1327079-1327558 > > chr1:1332147-1332266 > > chr1:167721383-167721592 > > chr1:181025469-181025588 > > chr1:19076253-19076372 > > chr1:19088429-19088548 > > chr1:19101541-19101660 > > > > > > Thanks > > > > > > Valeria Vasta > > Assay Development Scientist | Biochemical and Molecular Genetics R&D > > Seattle Children's Research Institute > > 206-884-7674 OFFICE > > 206-987-7660 FAX > > [email protected] > > OFFICE 1900 9th Ave, Seattle, WA 98101 > > MAIL C9S-9 > > WWW seattlechildrens.org<http://seattlechildrens.org/> > > > > > > CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is > for the sole use of the intended recipient(s) and may contain confidential > and privileged information protected by law. Any unauthorized review, use, > disclosure or distribution is prohibited. If you are not the intended > recipient, please contact the sender by reply e-mail and destroy all copies > of the original message. > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
