Hi Ya, > Could I also download Neanderthal genomes remapped to hg19 in bam files? Yes, see: ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/neandertal/seqAlis/ (we are working on adding links to hg19 downloads to the Neandertal portal page).
> Are they remapped to both hg19 human and chimpanzee genomes? The original mappings are to hg18 (human) and panTro2 (chimpanzee). The data were remapped to hg19 (human), but not to panTro3 (chimpanzee). I hope this is helpful. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 07/10/11 05:20, Ya Hu wrote: > Hi Brooke, > > Could I also download Neanderthal genomes remapped to hg19 in bam files? > Are they remapped to both hg19 human and chimpanzee genomes? > Many thanks, > Ya > > On Thu, Jul 7, 2011 at 3:15 AM, Brooke Rhead <[email protected]> wrote: > >> Hello Ya, >> >> The file you specified contains alignments of neandertal to panTro2. >> >> In addition to the track description Luvina linked you to, you might want >> to check out the Neandertal portal on the Genome Browser for an overview of >> available data: >> >> http://genome.ucsc.edu/**Neandertal/ <http://genome.ucsc.edu/Neandertal/> >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> >> On 07/01/11 23:58, Ya Hu wrote: >> >>> I learned from website all data were remapped to hg19, >>> >>> please ask whether the Neanderthal Contigs in >>> >>> ftp://hgdownload.cse.ucsc.edu/**gbdb/panTro2/neandertal/** >>> seqAlis/all-pt2.bam<ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/all-pt2.bam> >>> >>> from hg18/panTro2 or from hg19/panTro3? >>> >>> On Sat, Jul 2, 2011 at 7:15 AM, Luvina Guruvadoo <[email protected] >>>> wrote: >>> Hi Ya, >>>> You can refer to the track description page for more information on the >>>> Neanderthal Sequence Contigs: http://genome.ucsc.edu/cgi-** >>>> bin/hgTrackUi?g=ntSeqContigs&****db=panTro2<http://genome.** >>>> ucsc.edu/cgi-bin/hgTrackUi?g=**ntSeqContigs&db=panTro2<http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=ntSeqContigs&db=panTro2> >>>> >>>> Please contact us again at [email protected] if you have any further >>>> questions. >>>> >>>> --- >>>> Luvina Guruvadoo >>>> UCSC Genome Bioinformatics Group >>>> >>>> >>>> >>>> On 7/1/2011 7:50 AM, Ya Hu wrote: >>>> >>>> Dear sir or madam, >>>>> I currently downloaded Neanderthal sequence contigs from: >>>>> >>>>> ftp://hgdownload.cse.ucsc.edu/****gbdb/panTro2/neandertal/**<ftp://hgdownload.cse.ucsc.edu/**gbdb/panTro2/neandertal/**> >>>>> seqAlis/all-pt2.bam<ftp://**hgdownload.cse.ucsc.edu/gbdb/** >>>>> panTro2/neandertal/seqAlis/**all-pt2.bam<ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/all-pt2.bam> >>>>> >>>>> >From original paper (Green et al. 2010) one section describes further >>>>> processing of Neanderthal sequences as: >>>>> >>>>> >>>>> 1. We required that all reads map to the PanTro2 chimpanzee genome >>>>> sequence. >>>>> >>>>> 2. We required there to be no insertion/deletion polymorphisms when >>>>> aligned >>>>> to chimpanzee. >>>>> >>>>> 3. We restricted to autosomal reads. >>>>> >>>>> 4. We required that no more than 10% of bases in the reads disagree with >>>>> chimpanzee. >>>>> >>>>> 5. We only accepted nucleotides with a map quality (MAPQ) of at least 43 >>>>> as >>>>> assessed by the ANFO >>>>> >>>>> software, which is specialized for mapping ancient DNA reads ( >>>>> >>>>> *S13*). >>>>> >>>>> 6. We did not analyze nucleotides within 5bp of either end of the >>>>> Neandertal >>>>> read, because it is known >>>>> >>>>> that sequence quality is lower in these regions ( >>>>> >>>>> *S28*). >>>>> >>>>> >>>>> >>>>> Please ask whether current Neanderthal data are results of above >>>>> processes? >>>>> >>>>> Many thanks, >>>>> >>>>> Ya >>>>> ______________________________****_________________ >>>>> Genome maillist - [email protected] >>>>> https://lists.soe.ucsc.edu/****mailman/listinfo/genome<https://lists.soe.ucsc.edu/**mailman/listinfo/genome> >>>>> <https:**//lists.soe.ucsc.edu/mailman/**listinfo/genome<https://lists.soe.ucsc.edu/mailman/listinfo/genome> >>>>> >>>>> >>>> ______________________________**_________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/**mailman/listinfo/genome<https://lists.soe.ucsc.edu/mailman/listinfo/genome> >>> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
