Hi Chunjiang, The score of each base isn't actually in the table. The best place to obtain the score information is from the files in the following directory: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phyloP46way/placentalMammals/ For downloading large or multiple files, please see our recommended methods in the readme.txt file: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phyloP46way/README.txt
This directory contains the original ascii files that we translated (via wigEncode) into the wiggle track data. These files are the best source for the actual values at each base since the wigEncode procedure introduces its own reduction in precision, as explained: http://genomewiki.ucsc.edu/index.php/Wiggle To answer your second question, strand has no meaning in these phyloP tables. A conserved base prediction is simply a prediction of a conserved base; it is the same base in forward or reverse strand. I hope this information is helpful. Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group chunjiang he wrote, On 3/4/2011 12:06 PM: > Dear Mr/Ms, > > I want to ask which score can be used to represent conservation in > phyloP46wayPlacental. > I check it has a title like this: > *chrom* > *chromStart* > *chromEnd* > *lowerLimit* > *dataRange* > *validCount* > *sumData* > *sumSquares* > But I am not sure which column is the most important one i should use. > I see it is different to the paper they published. > > Another, I want to ask if the positive strand and negative strand in one > chromosome have the same genomic coordinates. > So here, the genomic coordinates are fit for both +/- strand? > > Thanks very much. > > Chunjiang > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
