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/ -- 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 > > 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> >> >> 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/** >>> 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> >>> >>> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
