Hello, Karen. The first thing I would like to point out is that there are three phastConsElements46way tables: primates, mammals and vertebrates. Your needs will dictate which one you will need to use.
For a detailed explanation of the Conservation score, see the Conserved Elements portion of the Methods section on the Conservation track description page here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way. The RepeatMasker track contains masked repeats and since you're looking for non-repeat masked regions, you are looking for the complement of these masked repeats. You can see a description of the RepeatMasker track here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=rmsk. If you trying to find where conserved regions overlap with non-repeat masked regions, you will need to create an intersection using our Table Browser. If you are unfamiliar with the Table Browser, please see the Table Browser User's Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. For an example of how to create an intersection using the Table Browser, see this previously-answered mailing list question: https://lists.soe.ucsc.edu/pipermail/genome/2012-January/028093.html. One important difference from this mailing list question is that when creating your intersection, you will need to also select the "All phastConsElements46way records that have no overlap with RepeatMasker" option in step 4 so that you are intersecting the phastCons data with all the regions not contained in the RepeatMasker track. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Liu, Karen Sent: Wednesday, February 15, 2012 2:14 PM To: [email protected] Subject: [Genome] question about annotation Hi, I am new to UCSC genome browser, but have read the user guide and searched through some forums. I still have a short question and hope it won't take up too much of your time. I'm looking for an annotation file of some sort to define all conserved regions (i.e. conservation score) and regulatory non-repeat masked regions. For conserved regions, would the table phastConsElements46way be a good source? Is the score in there conservation score? I don't know where I can find the non-repeat masked regions. If you could give me some pointers, it would be great. Thank you! Karen _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
