How to add a new reference genome to your genome database ? Urgent, thanks.

[Hakim Mireau]

Hello,

We are currently submitting an article to Nucleic Acids Research.

This is a Riboseq study based on Arabidopsis mitochondria and we need, prior to the submission, to map and provide a graphical view of our reads to a reference genome present on your server.

HOWEVER, your genome datable contains only the mitochondrial genome of the C24 Arabidopsis line (this is coming from the TAIR database). As most Arabidopsis labs, our analysis was performed on the Col-0 Arabidopsis line.

Unfortunately, the mitochondrial genomes of these two Arabidopsis lines have very different global organisations. Subsequently, the alignments we made make no sense since we have lots of cases where reads fall outside of mitochondrial coding sequences.

Here is my question: would it be possible to add the mitochondrial genome of the Col-0 Arabidopsis line to your database ? If so can you tell me how to do it ?

This genome has been sequenced and we have made a gff file for it.

Thanks for your help,

H. Mireau

INRA Center of Versailles

France

[Hakim Mireau]

Hi,

Could you please tell me if one can add a custom genome to your database ? If so, how we could do this ?

Effectively, the one you propose for Arabidopsis mitochondria is not compatible with our Riboseq data and the Nucleic Acids Research journal urge us to provide sequence alignments using your genome browser.

Our paper is under revision and we need an urgent answer from you please.

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sorry for the delay in my response.

Our grant specifies that we focus our efforts on vertebrate genomes, so we do not have the resources to add these genomes internally, but we still have a mechanism in place to make them available through external hosting and support.

Our assembly hub feature allows users to host their genomes and related annotations on a publicly-accessible web server, and then use the UCSC Genome Browser to visualize these annotations. You can find information about creating assembly hubs on the following help pages:

• Assembly hub wiki page
• Using UCSC Genome Browser Track Hubs
• Quick Start Guide to Assembly Hubs
• Help for Nucleic Acids Research submitters

Please review this previously answered mailing list question for additional information on creating and maintaining assembly hubs:

• https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/ozSm1vjaxRY/yZNRpWHRcvQJ

If you build an assembly hub for your genome following the steps above, we could then add a link on our Public Hubs page making it available for everyone.

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.

Jairo Navarro 
UCSC Genomics Institute

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