Hi Dave, You can retrieve this information using the Table Browser. Click on "Tables" (located on the top blue navigation bar). After selecting a clade, genome, and assembly of your choice, make the following selections:
group: Comparative Genomics track: Conservation table: choose one of the phyloP* tables region: click on 'define regions', from here you can paste or upload a list of regions, click 'submit' output format: data points output file: enter a filename to save results to a file, or leave blank (results displayed in browser) file type returned: plain text Click "get output". For more information on how to use the Table Browser, please see: http://genome.ucsc.edu/cgi-bin/hgTables#Help Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group PKDK wrote: > Hello > > I need to find a way to extract the phyloP conservation data for > specific areas of the chromosome. I have over 3000 specific areas that > I need to look at and extract the phyloP values for them. I thought > that I could just download the mass data file but it seems like the > file does not take into account gaps or areas on the chromosome where > the phyloP data is not given. > > For example if I wanted the following phyloP for the query : > chr1:1220332130-1220332150 > > On the large phyloP file the data for chr1, it starts at 10918. If > there are any gaps between 10918 and 1220332130, then the index to the > nucleotide number will be thrown off. Is there any way to compensate > for gaps? > > Or is there a better way to extract phyloP data? > > Thanks in advance > > Dave > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
