Hi Hong, You will also need to turn on "Element Conservation (phastCons)" located at the top of the track description page (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way); it is set to "hide" by default. Select a display mode from the drop down list and you should be able to view it in the browser.
Regards, --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 8/25/2011 9:41 AM, Hong Lu wrote: > 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
