Hello Jing, For the phastCons elements themselves, there are two methods to obtain the data:
1) Use the Table browser and choose track=Conservation and a table named like=phastConsElements46way*. With the table selected, click on "describe table schema" for the file format definition. This would be the quickest method to extract specific, limited regions. For the entire dataset, use method #2 (next). Example for hg19 region=chr21:33031597-33041570 output: #bin chrom chromStart chromEnd name score 837 chr21 33038756 33038841 lod=33 347 837 chr21 33038999 33039166 lod=42 383 837 chr21 33039861 33039908 lod=14 220 837 chr21 33040771 33041083 lod=60 435 2) Ftp from the Downloads server. Location: species -> assembly -> Annotation Database -> table_name.txt.gz For hg19, the file(s) would be in this location for ftp: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ (once connected to ftp server, cd to goldenPath/hg19/database) Hopefully this is the data you are seeking, but please let us know if you need further assistance or if you question has been misunderstood, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/26/10 9:56 AM, Jing Zhang wrote: > Hello, > > This is Jing from USC. I have a question regarding the Phastcons data in the > UCSC Genome Browser database. I can find the conservation scores from the > FTP. However, would you please help me to find the conserved elements > coordinates? The original paper mentioned that they have such information > uploaded to UCSC Genome Browser. Many thanks in advance. > > Best, > Jing > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
