Hi Brooke, Thanks once again for the prompt reply!
On Monday, February 06, 2012 03:55:36 PM Brooke Rhead wrote: > Hi Ivan, > > I can confirm for you that the CDS FASTA download files at > /goldenPath/hg19/multiz46way/alignments/known*.exon*.fa.gz files are > updated to correspond to the new UCSC Genes track set. Perfect, these are the files we use in our pipeline in conjunction with the knownGene track. > We didn't change the gene annotations for the Conservation track (used > to do the codon translation in the maf display), so they may not match > what's in the CDS FASTA files. That's fine by me, we do not use conservation track very much at the moment. Would be nice to have it updated eventually too of course. > Is there any other data you are wondering about? Well, I assume the same phylogenetic tree was used for the updated alignments. However, the Wiki article to which README links: http://genomewiki.ucsc.edu/index.php/Human/hg19/GRCh37_46- way_multiple_alignment Was never very clear about exactly which of the trees (original or corrected one) was actually used to produce final version of the alignments available for downloading. Would it be possible to elucidate now? Thanks, Ivan > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > On 2/3/12 11:46 AM, Ivan Adzhubey wrote: > > Hi, > > > > I have check GB downloads section on the production server and it looks > > like all of the > > /goldenPath/hg19/multiz46way/alignments/known*.exon*.fa.gz files have > > been updated already, now listed with the timestamps from 06-Jan-2012. > > > > I would appreciate if someone at UCSC GB team could confirm the updated > > MZ alignments release and provide details of what was updated and how > > (and what wasn't). > > > > Thank you, > > Ivan > > > > On Thursday 02 February 2012 11:26:35 pm Ivan Adzhubey wrote: > >> On Thursday, February 02, 2012 10:49:28 PM Donna Karolchik wrote: > >>> We're happy to announce the release of an updated UCSC Genes track > >>> for the GRCh37/hg19 human Genome Browser. > >> > >> Wow, congratulations! This new release looks like a massive effort. One > >> question: do you have plans to also update MultiZ alignments to match > >> the new transcript annotations? > >> > >> Thanks, > >> Ivan > >> _______________________________________________ > >> Genome maillist - [email protected] > >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > > The information in this e-mail is intended only for the person to whom it > > is addressed. If you believe this e-mail was sent to you in error and > > the e-mail contains patient information, please contact the Partners > > Compliance HelpLine at http://www.partners.org/complianceline . If the > > e-mail was sent to you in error but does not contain patient > > information, please contact the sender and properly dispose of the > > e-mail. > > > > > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome -- Ivan Adzhubey, Ph.D. Instructor Genetics Division, Brigham & Women's Hospital Harvard Medical School HMS New Research Building, Room 0464C 77 Avenue Louis Pasteur Boston, MA 02115 tel.: (617) 525-4728 fax: (617) 525-4705 web: http://genetics.bwh.harvard.edu/genetics/members/Ivan_Adzhubey.html _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
