Hi. I am currently analysing variation data of various species. I first worked on 1000 genome data, for which I downloaded the vcf files (from 1000 genomes) and then filtered out all non-coding sequences. I did this using exon coorindates downloaded from the UCSC table browser (in .bed format).
Now I am trying to do the same thing for Denisovan and Altai Neanderthal variation data (downloaded from here: http://cdna.eva.mpg.de/neandertal/altai/). However, UCSC does not appear to provide table browser data for either species, and I cannot locate exon co-ordinates anywhere.
The site that provides the data does have exome data (here: http://cdna.eva.mpg.de/neandertal/exomes/). However, the .bed file contains the coordinates of the longest transcript of the protein-coding genes analyzed in El Sidron, Vindija and Altai Neandertals all in one file. As such I cannot isolate the Altai Neanderthal exon co-ordinates. There is also nothing there for Denisovans.
Is anyone able to point me in the right direction for the exon co-orindates, or if not an alternative approach? Many thanks.