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
