Good Afternoon Graham: You can pick up the original files with the phyloP scores at: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phyloP46way/
These are the simple ASCII files before they are converted into compressed binary format to be used in the genome browser. You can use the binary format files too if that is convenient, please note: http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database I don't know if these are the numbers you are referring to, but these are the positive/negative actual phyloP calculated numbers. --Hiram ----- Original Message ----- From: "Graham Bignell" <[email protected]> To: [email protected] Sent: Thursday, May 17, 2012 7:45:51 AM Subject: [Genome] PhyloP plots in the UCSC browser Dear Jennifer, I am very interested in using the phyloP data from the UCSC genome browser as a way of assigning significance to putative somatic variants for a series of unmatched samples for which we have exome sequence data. I have downloaded the phyloP data from you ftp server for both the placental mammels and all vertebrate alignments, and have also looked through the paper cited on your web page (Detection of nonneutral substitution rates on mammalian phylogenies, Pollard-K et al). In the supplementary information associated with the paper there is a section on 'estimation of neutral model' which describes how the base level P-value data available from your FTP site was converted into the data presented in your browser track showing positive and negative scores (indicating conserved and vast evolving residues respectively). However, the conversion is going to difficult for me to apply! Do you have or could you possibly produce, a file that I can access which gives the base level values converted as described above and as presented in your browser, or possibly a script that allows me to do the relevant conversion to the files I have downloaded? I am sorry to have to approach you in this regard, I am associated with extensive amounts of data available to the research community via our web pages and know how time consuming these queries can be! Sincerely Graham Bignell Graham R. Bignell BSc. PhD. Senior Staff Scientist. Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust genome Campus, Hinxton, Cambridge, CB10 1SA. Tel +44 (0)1223 494818 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
