Hi Vikram, I have just been informed by one of our developers, Hiram, that:
"Actually, they are not out of date. Yes, they are incorrect, the correct one is: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/46way.corrected.nh But, the phastCons and phyloP data tracks were *not* recomputed after the corrected tree was determined. Experiments were done to demonstrate that the corrected tree did not make any difference of note in the phyloP and phastCons data. Therefore, the .mod files found in those directories are actually the files that were used. Placing a "corrected" .mod file there would be misleading. The notes about this correction are in the README file of: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/ " I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 9/28/10 12:36 PM, Vikram Agarwal wrote: > Hello, > > I noticed that the online version of the neutral .mod file for > vertebrates > (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/vertebrate.mod) > is the outdated one in which baboon and wallaby are listed as > outgroups. Could your group provide the updated one by any chance? > This was corrected online for the tree (as described in the erratum of > http://genomewiki.ucsc.edu/index.php/Human/hg19/GRCh37_46-way_multiple_alignment) > but not for the phastCons .mod parameter files provided. > > Thank you, > Vikram > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
