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