Hi Eric, You can upload a larger list of coordinates as a custom track. Hit the "add custom tracks" on the Genome Browser or Table Browser page, and choose your BED file to upload where it says "Paste URLs or data . . . Or upload:".
Now go back to the Table Browser and select the gene track you would like to get annotations from. Make sure "region: genome" is selected. Hit the "intersection: create" button and choose the custom track you uploaded. Choose to get all gene records that have any overlap with your custom track. Now you should be able to continue with your selections in the Table Browser as if you had defined a larger list of regions. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 3/1/12 12:42 PM, Eric Guo wrote: > Hi there, > > > I have a question regarding using a list of genome coordinates (in > the .bed format) to extract the name and annotations (exon, vs 3' > UTRs) from the table browser. The "define regions" option has a limit > of 1000 lines; however, my coordinate list is much long than 1000 > lines. I am wondering if there is another way to extract gene names > and annotations from a .bed file of genome coordinates. > > > Thanks in advance for your help. > > > -Eric _______________________________________________ Genome maillist > - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
