Conservation (I.E. Phastcons) Q

Question: Conservation (I.E. Phastcons) Q

6.3 years ago by

Hi All, I am using Galaxy (main) and would like to intersect a bed file I have with the PhastCons scores (primarily placental and primate). After much searching around I can't tell if these files are locally cached and if so how I access them. Alternatively I could get them directly from UCSC, but it seems like these files would be rather large and useful to other users as well. (I apologize if I am missing the obvious, I'm still a novice user.) I am using hg19, but of course could lift over to convert the coordinates. Best, Vinn Vincent J. Lynch, Ph.D. Associate Research Scientist Department of Ecology and Evolutionary Biology (EEB) & Yale Systems Biology Institute (YSBI) Yale University "There is a grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that whilst this planet has gone on cycling according to the fixed laws of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." -C. Darwin, 1859

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modified 6.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.3 years ago by Vincent Joseph Lynch • 40

6.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Vinn, The tools that work with this data are in the tool group "Get Genomic Scores". Currently, locally cached data is often based on older ENCODE datasets, hg17 for phastOdds, hg16/17/18 for Aggregate datapoints (the tool descriptions will note the exact datasets/genome versions). 1 - Lifting the query intervals is one option. 2 - Importing phastcons data for hg19 and using it from the history is another option when using the public Main Galaxy server. If you really need the entire genome, grouping the data by chromosome would be advised then loading into Galaxy using FTP, after downloading the data from the UCSC Downloads server: http://wiki.g2.bx.psu.edu/FTPUpload If you just need certain locations, the data can be exported from the UCSC Table browser to use with the "Aggregate datapoints" tool or as the actual result if BED coordinates are given (up to 1000). group: Comparative Genomics track: Conservation table: one of the "Cons" tables region: click on the position radio button and enter a single region or click on 'define' to enter up to 1000 regions in BED format. output format: data points send to Galaxy 3 - You could also set up a Local instance and load the data natively. http://getgalaxy.org If you need help tuning your Table Browser query or with the UCSC Downloads server the UCSC team is probably the best resource, but please let us know if we can help again, too: http://genome.ucsc.edu/contacts.html Hopefully this gets your project going! Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

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