Denisovan and Altai Neanderthal .bed files?
0
0
Entering edit mode
3.7 years ago
spiral01 ▴ 100

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.

snp • 1.2k views
ADD COMMENT
1
Entering edit mode

Just to clarify, the coordinates for the VCF files for the Neanderthal and Denisovan are computed on hg19. The coordinates should not be different.

ADD REPLY
0
Entering edit mode

Thank you. As the Neanderthal and Denisovan sequences are mapped to hg19, does this mean I can use the hg19 exome co-ordinates to filter my vcf files?

ADD REPLY
1
Entering edit mode

without knowing what you want to do exactly, yes, that would give you the exonic regions in the archaic humans.

ADD REPLY
0
Entering edit mode

Consider this: A: Looking for neanderthal genomes to download

I don't think you are going to find contiguous genome data for these ancient genomes.

ADD REPLY

Login before adding your answer.

Traffic: 1972 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6