How can one access the genome of Otzi the Iceman?

Question

[Larry_Parnell]

The genome of Ötzi the Iceman was sequenced and made available to the public via a browser. That browser was housed here but apparently is no longer available. Does anyone know where I can access or browse the genome from this 5,300-year-old Copper age individual? Many thanks!

Answer 1

[pld]

It is listed in the publication relating to the genetic analysis:

http://www.nature.com/ncomms/journal/v3/n2/full/ncomms1701.html

"Accession codes: The sequencing data have been uploaded to the European Nucleotide Archive under accession code ERP001144."

Answer 2

[5heikki]

Could have read the open access publication. Although you can't browse the genome as such but I'd guess that the bam files would enable that locally..

http://www.ebi.ac.uk/ena/data/view/ERP001144

[pld]

Got distracted reading the paper, you beat me!

[Larry_Parnell]

Thank you. What would be most helpful is a way to browse the genome so that I can go to a specific locus and examine the sequence in detail at that position/gene. The BAM and fastq files are not so useful to me.

[pld]

That is all that is there, the BAM files and the FastQ files and they're perfectly useful to your goals if you know how to use them. You could use IGV if you were to sort and convert the BAM into a SAM file, then move to your position of interest.

You could also generate a bed file for the regions you're interested in and use samtools view -b -L to generate a new bam file with only the regions in the bed file. That might make things a bit easier to manipulate.

[5heikki]

Wouldn't the bam files along with hg18 enable you to browse the genome in any standalone viewer?

[Larry_Parnell]

Thanks for your replies. Sure, the bam files loaded into a standalone genome viewer, which I currently do not have, would work, but that is all a bit much to do for a curiosity that is somewhere between way-back burner and hobby. I'm interested in just a dozen or so loci and hence my interest in the once-active browser.

[pld]

Most genome viewers are free.

[Larry_Parnell]

Thanks, I knew that. What is not free is my time for such an endeavor that is really quite beyond my main research focus. If this could be done in a few minutes, say by looking at the Ötzi viewer that once existed - fine. But that is not the case and so I must shelve this idea for another time, or for a student willing to learn something new. Again, thanks to you both for your responses.