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/vertebrate /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=cons46 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
