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How to sort chromosomes in Golden Helix Genome Browser?

asked 2017-10-15 18:35:10 -0700

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Dear,

I came across a problem that I don't know how to solve. I downloaded the new version of rainbow trout genome from NCBI website. I manually uploaded the FNA file of the genome into the Genome Browser. After I created the genome in the Genome Browse, the order of chromosomes was messed up. What shall I do to fix it?

My second question is that I uploaded a vcf file to the Genome Browser. Due to the different order of chromosomes between the created genome and vcf file, the Genome Browser cannot match up. Attached is the screenshot of the problem. I would be highly appreciated if you could help to solve the problems. Thank you very much. image description

Shawn

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answered 2017-11-09 15:06:56 -0700

SteveHystad gravatar image

Hi Shawn,

Was it the new Oncorhynchus mykiss (assembly Omyk_1.0) ?

If you add a FASTA file from a new assembly to Genomebrowse, an assembly file gets created which specifies the order of the chromosomes listed. By default these chromosomes are sorted by size and not by number. If you want to edit the order in which these are displayed, you will have to edit the assembly file. This is typically found in your user data folder. To access this folder from GenomeBrowse, you can click tools > Open Folder > Annotations folder. Then back-up one directory to find the Assemblies folder. you can open the assemblies file in a text editor and change the order of the chromosomes.

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FYI if you are interested in SVS (which has GenomeBrowse built-in) we can curate these assemblies for free!

SteveHystad ( 2017-11-09 15:07:45 -0700 )edit
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Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.

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Asked: 2017-10-15 18:35:10 -0700

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Last updated: Nov 09