Hi Kurinji, The best way to do this would be to create and upload a BED format custom track. This will allow you to upload all the genomic regions at once, and will also make navigation between the different regions easier by having them all listed and clickable within the custom track.
For more information on how to create a BED file, please see: http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED. For more general background on custom tracks, please see this help doc: http://genome.ucsc.edu/goldenPath/help/customTrack.html To view genes associated with these regions, you can turn on any of the gene prediction tracks, such as UCSC Genes, RefSeg Genes, Ensembl Genes, etc. to see where your regions map relative to the entries in these tracks. You can turn on any of these gene prediction tracks by scrolling down to "Gene and Gene Prediction Tracks" and selecting a display from the drop down list for the track you would like to use. I hope this helps. Please contact us again at [email protected] if you have any further questions. Best, Luvina --- Luvina Guruvadoo UCSC Genome Bioinformatics Group Kurinji Pandiyan wrote: > Hello, > > I have a file of 110 genomic regions in this format (chromosome > number:start:end). I want to find which of these regions have genes > associated with them and what genes. These regions were annotated using > HG18. I am unsure where and how to, on the UCSC browser, upload my xls/txt > file with these coordinates to retrieve a set of genes names associated with > these regions. I just don't want to do these manually, by entering the > information one by one. Any help to make this high throughput will be much > appreciated. > > Thank you very much! > Kurinji > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
