Thank you! On Tue, Jul 12, 2011 at 6:44 AM, Brooke Rhead <[email protected]> wrote:
> 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/<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/>< >>> 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/**<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 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://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/**> >>>>>> **<ftp://hgdownload.cse.ucsc.**edu/**gbdb/panTro2/neandertal/****<ftp://hgdownload.cse.ucsc.edu/**gbdb/panTro2/neandertal/**> >>>>>> > >>>>>> >>>>>> seqAlis/all-pt2.bam<ftp://**hg**download.cse.ucsc.edu/gbdb/**<http://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> >>>>>> > >>>>>> <https:**//lists.soe.ucsc.edu/**mailman/**listinfo/genome<http://lists.soe.ucsc.edu/mailman/**listinfo/genome> >>>>>> <http**s://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> >>>> <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
