Hi Luvina, Thank you for your reply.
To display "Vertebrate Conservation by PhastCons" within the browser, I select the "Vertebrate". The row " Vertebrate Cons Vertebrate Conservation by PhastCons " is marked as selected. But the number of selected (at the bottom of this section) is still " 2 of 10 selected", which means the row " Vertebrate Cons Vertebrate Conservation by PhastCons " does not count as selected. And also, when I click the "Submit" button, only "Conservation by PhyloP" is displayed. I cannot find the value/curve of "Conservation by PhastCons"? Would you please give me some suggestion? Thanks. Best, Hong -----Original Message----- From: Luvina Guruvadoo [mailto:[email protected]] Sent: Wednesday, August 24, 2011 11:43 AM To: Hong Lu Cc: [email protected] Subject: Re: [Genome] Two questions on conservation score from UCSC browser Hi Hong, PhyloP and PhastCons are two different processes using different mathematical models, so all the bases in one system may not have corresponding values in the second system. You can read more about these two procedures in the track description page found here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way. The "PhastCons Conservation" and "PhyloP Conservation" sections also provide citations and URLs to additional resources. To display "Vertebrate Conservation by PhastCons" within the browser, select the "Vertebrate" checkbox under "Select subtracks by clade:". I hope this helps. Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 8/23/2011 3:20 PM, Hong Lu wrote: > Hello, > > > > This is Hong Lu, a bioinformatics scientist from Ambry Genetics. > > > > I am interested in the conservation score from UCSC. I downloaded > those data from the following link. > > phyloP: > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phyloP46way/vertebrate/ > ch > rY.phyloP46way.wigFix.gz > > phastCons: > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/vertebra > te > /chrY.phastCons46way.wigFix.gz > > > > The structure of files is as below > > ================================== > > fixedStep chrom=chrY start=10502 step=1 > > 0.371 > > 0.371 > > 0.325 > > ================================== > > The number 10502 is the start position of this block. > > > > At most cases, the title, eg "fixedStep chrom=chrY start=10502 step=1" > is same for phyloP and phastCons results. > > > > But sometimes, they are different. For example. > > In "chr18.phyloP46way.wigFix" > > fixedStep chrom=chr18 start=73384641 step=1 > > In "chr18.phastCons46way.wigFix" > > fixedStep chrom=chr18 start=73384640 step=1 > > > > It's always 1 bp difference. Those cases happen at chr1, chr17 and > chr18. For other chromosomes, they are exactly same. > > > > Would you please tell me the reason of this problem? Thanks. > > > > And also, in the genome browser, how to show the "Vertebrate > Conservation by PhastCons"? The checkbox is grey and unclickable. > > Eg: > http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=208545387&c=chr6&g=cons > 46 > way > > > > Thank you and have a nice day! > > > > Hong Lu > > > > Bioinformatics Scientist > > [email protected] > > 949-900-5544 > > 515-450-8095 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
