stickleback genome

[Kostas Sagonas]

Dear Sir/Madam,

My name is Konstantinos Sagonas and I am a researcher in QMUL in London. I use the three-spined
stickleback to address evolutionary genomic questions and therefore I am interesting in using the Stickleback
genome [Feb. 2006 (Broad/gasAcu1)] available in your website. However, because I cannot access the project
website (http://www.broad.mit.edu/tools/data/data-vert.html) I was wondering if you could help me understand
how this assembly is different from the current ENSEMBL one and whether you keep it updated.

Thank you very much for your time and consideration

Kind regards,
Kostas

[Cath Tyner]

Hello Kostas,

Thank you for contacting the UCSC Genome Browser support team and inquiring about the gasAcu1 assembly. 

One of our developers has shared the following. If you have further questions, please respond to this list so that we can provide assistance. 

There is only one single NCBI/Genbank Stickleback assembly:

GCA_000180675.1/ASM18067v1

from 2006.

https://www.ncbi.nlm.nih.gov/assembly/GCA_000180675.1/

However, that assembly appears to have no relationship either

to the UCSC assembly or the Ensembl assembly. And appearances are

deceiving.

Both Ensembl and UCSC have identical chromosome sequences.

The chrom names at Ensembl are group[romanNumerals] where

UCSC has chrom[romanNumerals]

The Genbank assembly is contigs only, no larger than 698,234 bases.

Ensembl has a mix is scaffolds and contigs in addition to the chromosomes.

UCSC has contigs combined into a single artificial chrUn.

It is possible to relate most of the contigs and scaffolds to each

other in the three assemblies. It is not a straightforward process.

Thank you for contacting the UCSC Genome Browser support team. 

​

Please send new and follow-up questions to one of our mailing lists below:

  * Post to the Public Help Forum: E

mail 

gen...@soe.ucsc.edu

​ or search the Public Archives

​  * Post to the Mirror Help Forum: Email

 genome...@soe.ucsc.edu 

or search the Mirror Archives​

​  * Confidential/private help: Email

 genom...@soe.ucsc.edu

Join us on Social Media! Facebook, Twitter, Wordpress Blog, YouTube

UCSC Genome Browser Announcements List (for new data & software)

Request on-site training & workshops at your institution

​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

--

---
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 post to this group, send email to gen...@soe.ucsc.edu.
Visit this group at https://groups.google.com/a/soe.ucsc.edu/group/genome/.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/0de46e93-ff8c-4acf-bd75-218f3a0650a7%40qmul.ac.uk.
For more options, visit https://groups.google.com/a/soe.ucsc.edu/d/optout.