Kim,
The details pages for the conservation track has a lot of the information you are looking for, such as description of phylop and phastcons. Look under "description" and "methods": http://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chrX&g=cons44way This previously answered mailing list question should help with step-by-step instructions for obtaining a conservation score for each of your SNPs: https://lists.soe.ucsc.edu/pipermail/genome/2006-February/009816.html You can zoom in on an individual SNP, and if you have the Conservation track turned on as well, you can visually inspect what the conservation is looking like in that region. The Galaxy website has some tools which look like they might be useful to you. If you click on the following link and then click on "Get Genomic Scores", some of the subsections are related to phastCons: http://main.g2.bx.psu.edu/ I hope this information is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group ----- "Kim" <[email protected]> wrote: > Dear group members, I have several questions I am trying to get help > with: > > step 5 in this message > (https://lists.soe.ucsc.edu/pipermail/genome/2006-February/009806.html) > says > > "5. Go back up to group: and change it to "Comparative Genomics", > track: > Conservation, table: multiz8way." All is good except under table > header I see three options: > > 1) Mammal Cons (phylo44wayPlacMammal) > > 2) Mammal Cons (phastCons44wayPlacentak) and > > 3) Mammal El (phastConsElements44wayPlacental) > > I am trying to find conservation score for some human SNPs. Which one > would be the best? > > ------------------ > I have a BED file of my SNPs (only 4 columns: chr, start, end, name) > that I would like to intersect with one of the phastCons files above > to get conservation scores for my SNPs. Can someone provide me with > step-by-step instructions? > > ------------ > Is there a way I can see conservation score of a single SNP on UCSC > genome browser just to be sure I am getting correct scores if I > successfully download the scores using intersecting tables? > > ------------- > I am trying to find proximity of my SNPs to CpG islands. Can someone > provide me with instructions on how to upload my list of files and get > the proximity. Sorry that I just a beginner so step-by-step > instructions would be very helpful. > > I hope these are not too much to ask. Thank you very much for all the > great help. > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
