Dear Vanessa and Katrina, Very appreciate to your answer. Now I think I can get conservation score for each base in genome. And I see there are many gaps at each chromosome result. I still have two questions about this work.
1. I see the phastcons and phylop both provide the conservation score for each base. So which one is better when I apply them at a small speical genome region, eg. length of 100~200bp. 2. I see both phylop and phastcons used 46way in human and 30way in mouse prediction. In human, there are 22 autosomes and in mouse there are 19 autosomes. So If the conservation score come from alignment between different speices, how do they get the conservation info in human chromosome 20, 21 and 22. And similar, for other speices that there are not enough chromosomes comparing to human, how to understand the conservation score at human chromosomes. Thanks so much again. Best, Chunjiang In Thu, Mar 24, 2011 at 2:32 PM, Vanessa Kirkup Swing <[email protected]>wrote: > Dear Chunjiang, > > Here is a previously answered question about calculating the conservation > score in a region: > > https://lists.soe.ucsc.edu/pipermail/genome/2010-November/024065.html > > In this case you don't need to be concerned about how to calculate the > reverse strand coordinates. My colleague answered this in one of your > earlier questions: > > > 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 that this helps to clarify things for you. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > ----- Original Message ----- > From: "chunjiang he" <[email protected]> > To: "Vanessa Kirkup Swing" <[email protected]> > Cc: [email protected] > Sent: Thursday, March 24, 2011 9:11:08 AM > Subject: Re: [Genome] a question about phylop conservation > > > > Dear Dr. Swing, > > Thanks for your guide. As your answer, I am still a little confused about > how to caculate the conservation score in a multiple bases region when I > only have the 1-base step scores. > I see there is 'span' parameter but I dont know how to use that from the > table files. > > fixedStep chrom=chr1 start=10918 step=1 > 0.064 > 0.056 > 0.064 > > I can't find the answer from > http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way > > Another, I see chromsize is used to caculate the reverse strand > coordinates. So how I can get the chromsize for each chromosome. > > Thanks again, > > Best, > Chunjiang > > > On Wed, Mar 9, 2011 at 12:14 PM, Vanessa Kirkup Swing < > [email protected] > wrote: > > > 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
