chicken genome

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Li, Xin

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Jul 25, 2016, 10:42:58 AM7/25/16
to gen...@soe.ucsc.edu
UCSC Genome Informatics Group,

I am writing to inquire when UCSC will add the Gallus_gallus-5.0 assembly into the bowser. It was released in 2015/12/16. Could you please let me know whether that will happen recently? 


Thank you. 

Xin

Xin Zhiguo Li, Ph.D.
Assistant Professor
University of Rochester Center for RNA Biology: From Genome to Therapeutics
Department of Biochemistry and Biophysics
Department of Urology
Box 712, Rm 3-8553
University of Rochester
601 Elmwood Ave
Rochester, NY, 14642
Phone: 585-275-6576

Christopher Lee

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Jul 27, 2016, 12:27:25 PM7/27/16
to Li, Xin, gen...@soe.ucsc.edu

Hi Xin,

We may have the galGal5 assembly​ and downloads​ available at the UCSC Genome Browser at a later time, but it is not currently on the list of assemblies we are planning to release​ in the near future​.

In the meantime, you can find galGal5 as part of an assembly hub​, where you will also find information for downloads, at http://genome-preview.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-preview.cse.ucsc.edu/gbdb/hubs/genbank/vertebrate_other/hub.txt&genome=GCA_000002315.3_Gallus_gallus-5.0

Please note that this hub is not an official UCSC Genome Browser assembly, therefore it​ ​does not include all of the typical download files associated with an official assembly.

You can also view galGal5​ ​on our​ ​preview site at http://genome-preview.cse.ucsc.edu/cgi-bin/hgGateway?db=galGal5

Please note the warning at our preview site​:​
WARNING: This is the UCSC Genome Browser preview site. This website is a weekly mirror of our internal development server for public access. Data and tools on this site are under development, have not been reviewed for quality, and are subject to change at any time. We provide this site for early access, with the warning that it is less available and stable than our public site. The high-quality, reviewed public site of the UCSC Genome Browser is available for use at http://genome.ucsc.edu/.

Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data, you may send it instead
to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute


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Li, Xin

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Jul 28, 2016, 12:02:57 PM7/28/16
to Christopher Lee, gen...@soe.ucsc.edu
Christopher Lee, 

Thank you for your reply and sharing with me the preview. I saw in the preview the repeat masker file has been uploaded. Could you please comments on whether there is ongoing effort to further refine it and whether there is plan to update that part recently? 

Kind Regards!

Xin

Luvina Guruvadoo

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Jul 29, 2016, 11:14:20 AM7/29/16
to Li, Xin, Christopher Lee, gen...@soe.ucsc.edu
Hello Xin,

As my colleague Christopher mentioned in his previous email, galGal5 is not currently on our list of assemblies we plan to release in the near future. Any files available on our preview server have not yet been reviewed by our Quality Assurance team and may undergo changes. At the moment we do not have plans to update the Repeat Masker data.

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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Regards,
Luvina

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Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu




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Li, Xin

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Aug 8, 2016, 11:44:06 AM8/8/16
to Luvina Guruvadoo, Christopher Lee, gen...@soe.ucsc.edu
Luvina, 

Thank you for your reply. I have downloaded files from the UCSC_gg5_preview, including the refseq, but could not find the genome fasta file. I therefore downloaded the genome fasta file of gg5 from NCBI but the naming of the unassembled chromosomes there do not match with the UCSC ones.

For example, the ones from the NCBI (http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/chicken/) called something like Chr8_AADN04000928v1_random, while the ones from UCSC called chr8_NT_461327v1_random. I was wondering whether UCSC can provide a link to download the genome fasta file of gg5 directly or refer me to someone who can help me with the name difference. 

Please excuse me for asking a lot for a preview assembly. We hit into something interesting on chicken viral defense and using accurate assembly is important to reveal this phenomenon. I appreciate your generous help. 

Xin

Christopher Lee

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Aug 11, 2016, 4:16:12 PM8/11/16
to Li, Xin, Luvina Guruvadoo, gen...@soe.ucsc.edu

Hi Xin,

Thank you for your question about galGal5 Fasta files. You can find the files you are looking for on our preview downloads server:
http://hgdownload-test.soe.ucsc.edu/goldenPath/galGal5/bigZips/galGal5.fa.gz

Please remember that any files available on our preview server have not yet been reviewed by our Quality Assurance team and may undergo changes.

Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data, you may send it instead
to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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