Thank you for your interest in the Genome Browser and for letting us know about the Chinese Hamster assembly (GCF_003668045.3).
We offer this Chinese Hamster assembly (GCF_003668045.3) as an assembly hub:
The supporting download files can be found here:
You can read about assembly hubs here: http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Thanks Gerardo and others!
But I am afraid I am still confused. The assembly that you pointed me to still does not appear to be chromosome level. It doesn't recognize "Chr2:" , etc and seems to be just showing just individual scaffolds of limited size if I search for a specific gene- ie HSPA1A. This is because the average scaffold sizes are quite small.
The article I attached previously used Hi-C and other methods
to align these scaffolds and group them onto chromosome-level
The NCBI lists a chromosome level assembly: CriGri-PICRH-1.0
with accession numbers:
I am looking for a way to visualize entire chromosomes at once. The 4D Nucleome data I visualize involves features such as LADs, NADs, TADs, etc which are larger than many of the scaffolds and we are interested in seeing many such consecutive features covering typically tens of Mbp or entire chromosome arms when we look at our data.
Thanks for following up to get clarity on this topic. The assembly we previously linked you to is exactly the one you requested, RefSeq Assembly Accession GCF_003668045.3. You can access this browser below:
Instead of using chromosome names (chr2), we use RefSeq names (NC_048595.1) because they are more universal across assemblies. This is something we're working on making more clear. You can see an equivalency table here, which means that searches or custom tracks with any of the names listed should work for this assembly:
For chromosome-scale visualization, you can zoom out to entire chromosomes. It may be slow to load if you have many tracks turned on, so I recommend keeping your tracks minimal or in "Dense" modes at first. I hope this is helpful!
All the best,
UCSC Genome Browser
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/387f0746-67fa-f422-4528-5adf983fe886%40illinois.edu.