Question for X. tropicals & X. laevis genome

[Taejoon Kwon]

Hi,

(1) New version of the Xenopus laevis genome is released a while ago,
but it is not available on the UCSC genome browser. Do you have any
plans to serve this version in the near future?

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_017654675.1/

(2) Multiple genome alignments were quite useful for xenTro9,
especially to improve the gene annotation.

http://hgdownload.soe.ucsc.edu/goldenPath/xenTro9/phyloP11way/
http://hgdownload.soe.ucsc.edu/goldenPath/xenTro9/phastCons11way/

But this is not available for new xenTro10 or X. laevis genome. Do you
have any plan to analyze them also?

Thank you for your help.

Best,

Taejoon

--
-=-=-=-=-=-=-=-
Taejoon Kwon, Ph.D <tk...@unist.ac.kr>

Assistant Professor
Department of Biomedical Engineering
School of Life Sciences
Ulsan National Institute of Science and Technology, Republic of Korea

http://www.taejoonlab.org/

[Maximilian Haeussler]

Hi Taejoon,

(1) if you type "Xenopus" into the search box on our genome gateway page http://genome.ucsc.edu/cgi-bin/hgGateway, you should be able to find it, here is the direct link: https://genome.ucsc.edu/h/GCF_017654675.1

(2) I believe that we should be able to create genome-genome alignments that you need for the new assembly, which ones do you need?

best
Max

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAGCz_Z8UqLt9TBTOug%2BmJf-gGP-gnE_-v3zWgwLFiKw31n%3DFiw%40mail.gmail.com.

[Taejoon Kwon]

Thank you so much, Max.

> (1) if you type "Xenopus" into the search box on our genome gateway page http://genome.ucsc.edu/cgi-bin/hgGateway, you should be able to find it, here is the direct link: https://genome.ucsc.edu/h/GCF_017654675.1

Great! Can I access these data via the FTP repository also? Also, I
am curious about its 'code name,' i.e., xenLae10.

> (2) I believe that we should be able to create genome-genome alignments that you need for the new assembly, which ones do you need?

I will discuss this with other researchers and let you know shortly.

Thank you so much!

Taejoon

--
--
-=-=-=-=-=-=-=-
Taejoon Kwon, Ph.D. <tk...@unist.ac.kr>

Associate Professor
Department of Biomedical Engineering,
College of Information-Bio Convergence Engineering,
Ulsan National Institute of Science and Technology (UNIST),

[Maximilian Haeussler]

Great! Can I access these data via the FTP repository also?  Also, I

Yes, you need to click "Genomes" in the top blue bar menu to find the page that mentions the FTP location:

https://genome.ucsc.edu/h/GCF_017654675.1

The FTP location is then shown in the description of this genome. We need to add a link that more clearly points to this page with the genome description.

 

> I am curious about its 'code name,' i.e., xenLae10.

This genome was imported from NCBI together with thousands of others, we do not define names for these anymore. It's best to use its NCBI accession to refer to it: GCF_017654675.1

I know, that's not very readable, but it'll make it very clear what the assembly is and all genomics resources seem to settle onto these identifiers now.

[Taejoon Kwon]

Dear Maximilian, 

A long time ago, I asked the question about genome-genome alignments & the conservation scores as below. 

xenTro9 has the results of 11ways of phastCons/multiz/phyloP at https://hgdownload.soe.ucsc.edu/goldenPath/xenTro9/

Can you create the same files for xenTro10? (I think the species used for xenTro9 will be OK).

Also, can you make the same files for X. laevis genome? https://genome.ucsc.edu/h/GCF_017654675.1

As you know, X. laevis has a genome duplication, so it has L/S chromosomes. 

If you can run the genome-genome analysis for those L/S chromosomes separately (like 1L, 2L, ..., 9_10L and 1S, 2S, ..., 9_10S are different species), it would be very useful for the Xenopus community. 

Another question. Where do you get the annotation files for X. laevis & X. tropicalis? From NCBI?

If you have a separate annotation pipeline (vs. NCBI or EnsEMBL), can I get the GFF3/GTF for that?

Thanks, 

Taejoon