Hi Nicholas, After testing several ways to do this, we recommend using the table browser (http://genome.ucsc.edu/cgi-bin/hgTables) and this method:
genome: Human assembly: hg19 group: Comparative Genomics track: Conservation table: Multiz Align (multiz46way) region: click "define regions" and paste in your coordinates. Note that you can only paste in 1000 regions. intersection: click "create". Choose a gene prediction track and choose the radio button " All multiz46way records that have *no* overlap with 'gene prediction track'". Click "submit". output file: enter a name if you want to save the output as a file and click "get output". I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 12/7/10 2:44 PM, Nicholas Price wrote: > Hi, > > I have the coordinates of Human pseudogenes and I want to use multiz46way to > get possible orthologs. However because pseudogenes are nonfunctional > I want to exclude regions that include exons...Is there a way to do that? > > Nicholas > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
