[Genome] changing your assembly reference

[Rachel Harte]

Hello Tony,
How are you? I would need to ask if you could create a new reference 
assembly for this - do you mean that you would like to be able to create 
it on our site?  I expect you just need to do it for one chromosome. You 
would need to add the information about the corrected region to the AGP 
file and incorporate the corrected sequence in the appropriate scaffold. 
I could help with that. You could always create a mirror site just for 
the one zebrafish chromosome with the incorrectly assembled region and 
then we could link to it. I know that GBrowse is a tool that people use 
for visualising genomes and tracks of sequence-related data. I will ask 
the Browser group and see if anyone has any other ideas.

Rachel

Anthony DiBiase wrote:
>
> We know the zebrafish assembly is incorrect for a specific gene locus 
> (approx. 250K basepairs).  Is there a way to load in our own (correct) 
> data for this locus as a new reference assembly (which we would then 
> make custom tracks against) ? 
>
>  
>
> If not possible with the UCSC genome browser, is there another tool 
> you'd recommend (e.g. Broad's Argo) ?
>
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-- 
Rachel Harte, Ph.D.
Bioinformatics Engineer
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu