ancient DNA

[Juergen Schmitz]

Hi Santa Cruz Team,
I am very frustrated to add consensus Neanderthal sequences to my genes. This worked perfectly one year ago, e.g., for FPR1 in human, but now I get no assemblies of ancient DNA or can't find the Group-box setting to add this for hg18, hg19, or hg38.
Could you please help me set this up? Best for hg38.
Many thanks,

Juergen

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[Maximilian Haeussler]

Hi, 

>  I have done this in UCSC hg18 with the settings in Neandertal Assembly and Analysis: Neandertal Cntgs.

I see, you mean this track: https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=ntSeqContigs&hgTracksConfigPage=configure

These are assembled sequences, the Neandertal groups are not making anything similar anymore, so we cannot show a track like this, they only publish variants.

> Is such a setting also available for Denisova? I think for hg38 is only variation available?

I don't know which setting you mean. Or what you mean with "setting". I went through all settings of this track and cannot find a setting that allows you to export hg18 sequence with the Neandertal variants in them.

I guess that you made your consensus sequences manually, by copy-pasting nucleotides? I am unaware of a feature that allows you to do this, add variants from these alignments to the hg18 sequence?

On hg38, we have a variants track, the "Ancient Hominids" track, aka ArcSeqHub, on hg38: 

https://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chr20&g=denisovan&db=hg38

Isn't that sufficient for what you need? Are you missing data or are you missing a software feature?

Sorry, I guess I don't understand your question. I understood that you want the cDNA sequence of a gene, with the Neandertal variants swapped into the human sequence, but I don't think we ever had such a feature? (my colleagues may confirm this or correct me)

best

Max 

On Sat, Jul 11, 2026 at 5:55 AM Jürgen Schmitz <jue...@uni-muenster.de> wrote:

Hi Max,

Thanks a lot for you response. I am comparing neutrophil genes in human populations and want to have an outgroup with Neanderthal sequences. I have done this in UCSC hg18 with the settings in Neandertal Assembly and Analysis: Neandertal Cntgs. Is such a setting also available for Denisova? I think for hg38 is only variation available?

I am very interested in an update of ancient data for my evolutionary study. Many greetings to the team. In the past I had many happy cooperations with UCSC:-)

Juergen

PS: the Neandertal data are noisy, therefore, as more, as better. Maybe you can add Ranis as well. Looks like a good quality 30.000 year ancient DNA. 

Sent from my iPad

Q

On 10. Jul 2026, at 22:53, Maximilian Haeussler <mhae...@ucsc.edu> wrote:



Hi Juergen,

can you give us a few more details? I don't know what you mean with "consensus sequences" (entire chromosomes?, single genes?), there are many ways to make consensus sequences and I don't remember that we have one. Maybe you mean our "View > DNA" feature and you configured that to highlight neanderthal sequences?

Neanderthal annotations for hg38 were added very recently, are you sure that you used that before? 

We know little about how Neanderthal data is used by researchers in practice, so any explanations helps us design our features for this use case.

Note that the MPI's Janet Kelso will send us another hg38 recompute soon. The arcseqhub that we have now has only two genomes, I think. Are you looking for a specific version of the data?

 

best

Max

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