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
