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
