Dear Chunjiang, See the answers below:
So should I treat the 0.064 as the conservation score of the base 10918? Yes, the coordinates for wiggle tracks are specified as 1-relative. For a chromosome of length N, the first position is 1 and the last position is N. Only positions specified have data. Here is more information on wiggle tracks: http://genome.ucsc.edu/goldenPath/help/wiggle.html If I want to get the conservation score from base 10918 to 10920, could I average the three scores "0.064,0.056,0.064" or by some other method? Please read the description page for this track and the papers that are referenced: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way And also, If I have a part of genome sequence located in: "chr1/- 1617197 1617281 " How could I get the conservation score of this part as it is on the reverse strand? If these coordinates are from the Genome Browser and not from a table they are 1-based. If they are from a table, they are 0-based. This will help explain our coordinate system: http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1 Here is information on how we calculate the reverse strand: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms Hope this helps! Please contact the mailing list if you have further questions. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "chunjiang he" <[email protected]> To: "Katrina Learned" <[email protected]> Cc: [email protected] Sent: Tuesday, March 8, 2011 3:29:38 PM Subject: Re: [Genome] a question about phylop conservation Thanks so much Katrina, So as you say, I get the file "chr1.phyloP46way.placental.wigFix" and open it. And I see the file like this "fixedStep chrom=chr1 start=10918 step=1 0.064 0.056 0.064 ... " . So should I treat the 0.064 as the conservation score of the base 10918? If I want to get the conservation score from base 10918 to 10920, could I average the three scores "0.064,0.056,0.064" or by some other method? And also, If I have a part of genome sequence located in: "chr1/- 1617197 1617281 " How could I get the conservation score of this part as it is on the reverse strand? Thanks again, Chunjiang On Tue, Mar 8, 2011 at 2:57 PM, Katrina Learned <[email protected]>wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
