Hello, The BAM file URLs for the Neandertal tracks are listed on the Neandertal gateway page (http://genome.ucsc.edu/Neandertal/). You can extract alignments in a region from a BAM file using samtools. For example, to see assembled contigs of Vi33.16 in the region chr1:1,000,001-1,005,000:
samtools view ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.16-hg18.bam chr1:1000000-1005000 Samtools stores the associated index file (Vi33.16-hg18.bam.bai) in your current working directory, to speed up subsequent accesses from the same working directory. Run "samtools view" with no other args to see usage. Samtools is available from http://samtools.sourceforge.net/ I hope this information is helpful. Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group [email protected] wrote, On 11/10/10 16:11: > How does one generate a human-Neanderthal DNA segment alignment? > Thanks. > GGoldberger > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
