Hi Tomas, Please see the answers to your questions below. If you have any additional questions, please contact us again: [email protected].
Regards, --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 10/3/2011 8:28 PM, Tomas Lovera wrote: > Hi Katrina, > > Thanks for your response. Would like to ask you some additional questions as > follows: > > 1.- Is there any plan to create the Modern Human Sequence and Neandertal > Contigs tracks on hg 19?. See answer to #5. > > 2.- Is there any plan to create the Denisova Assembly and Analysis Tracks on > hg19?. What would be the process to get this done? See answer to #5. > > 3.-Would like to know what is the difference between assembling (on hg 19) > and lifting over (from hg18) the Modern Human Sequence and Neandertal > (Denisova)Assembly and Analysis Tracks. One of our engineers has this to say: The contributors (Max Planck Institute) aligned Neandertal sequence reads to hg18, and then generated analysis tracks (Contigs, SNPs, signatures of selection etc.) from those alignments. For hg19, they did re-align the sequence reads, but they did not re-do all of the downstream analysis; that's why we resorted to liftOver for those. LiftOver uses alignments of hg18 to hg19 to translate coordinates, and it's not perfect but at least we can see most of the data on hg19. We currently don't have a way to LiftOver the contig alignments or Modern Human sequence alignments (BAM files; since those are alignments, it's really best for them to be regenerated on the new target assembly). > 4.- What are the reasons for the differences between Human DNA variants when > hg18 version is compared with the hg19 version. By "Human DNA variants", are you referring to the SNP track or differing bases between human and Neandertal? Small differences between hg18 vs. hg19 are not too surprising, but if there are major disagreements in some regions, please let us know and we can take a look. > 5.- Who is accountable for ensuring the DNA sequences alignment for Modern > Human, Neandertal and Denisova?. Ed Green and others at the Max Planck Institute have kindly provided the sequence alignment files for hg18 and hg19, as well was the analysis tracks for hg18. Here at UCSC, we do our best with limited resources to QA and provide liftOvers, etc. > > Thanks, Tomas > > ________________________________ > From: Katrina Learned<[email protected] sc.edu> > To: Tomas Lovera<[email protected]> > Cc: "[email protected]"<[email protected]> > Sent: Friday, September 30, 2011 8:53:41 AM > Subject: Re: [Genome] Neandertal and Denisova Assembly and Analysis Tracks. > > Hi Tomas, > > Most of the Neandertal Assembly and Analysis tracks are available on hg19. > The Modern Human Seq and Neandertal Contigs tracks are the only tracks from > this group that are only available on hg18 and not on hg19. Most of the > Neandertal tracks on hg19 were lifted over from hg18 and have a "18" icon > next to their names; for more information on tracks we've lifted, see > http://genome.ucsc.edu/goldenPath/help/hg18ToHg19LiftOver.html. > > To access these tracks on hg19, from the main browser page > (http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19), scroll down to the > "Neandertal Assembly and Analysis" group. > > The Denisova Assembly and Analysis tracks are not available on hg19. > > Please contact the mail list ([email protected]) again if you have any > further questions. > > Katrina Learned > UCSC Genome Bioinformatics Group > > > > On 9/29/11 11:45 PM, Tomas Lovera wrote: >> Dear, >> Can you please let me know whether the Neandertal and Denisova Assemblies >> and Analysis tracks are also available as part of the February 2009 >> GRCh37/hg 19 reference sequence? To access the Neandertal and Denisova >> Assemblies and Analysis tracks information,please click in the follopwing >> links: >> 1.- UCSC Genome and Bioinformatics Home Page >> 2.- Neandertal >> 3.- Neandertal Alleles in Human/ChimpCoding Non-synonymous Differences in >> Human Lineage: ........ >> 4.- All Neandertal Assembly and Analysis Tracks >> 5.- Configure Tracks on UCSC Genome Browser >> 6.- Neandertal Assembly and Analysis >> 7.- Denisova Assembly and Analysis >> Thanks, Tomas Lovera, >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
