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genome upload?

asked 2014-01-28 09:45:05 -0600

Olga Gonzalez gravatar image


I want to try your program but I work with the Human herpesvirus 8 (KSHV) and he genome is not available. How can I upload the genome into the browser?

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answered 2014-04-21 11:08:02 -0600

GenomeBrowse 2.0 has been released! You can download the most recent installer from our website.

Included in the new version is the ability to add custom genomes to GenomeBrowse. You can find full details in our new GenomeBrowse manual.

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answered 2014-01-29 13:12:38 -0600

Hi Olga,

Thank you for your questions.

To add a new genome to GenomeBrowse we require an assembly file for the species. This file is basically a list of the chromosomes (or scaffolds) for the genome build. You can find examples of how these files should be formatted in your Genome Maps folder for GenomeBrowse by going to Tools > Open Folder > Program Folder. With the correct assembly file you can visualize your BAM file data as long as you also have the corresponding index file (BAI).

If you do not have an index then your species will also need to have a reference sequence available in GenomeBrowse format (currently IDF soon to be TSF). These files can be created in our existing SVS7 software from FASTA files using our existing data conversion tool.

We are in the process of finishing up implementation of our new conversion tool for GenomeBrowse. The new tool will not only create the reference sequence tracks but will build the assembly file as well as annotation tracks from a variety of other sources (VCF, Text delimited, BED, WIG, GTF). Once the tool is complete we will then be releasing an update of GenomeBrowse (version 2.0) that includes this new feature.

The new version of GenomeBrowse is schedule for release in mid-March.

Thanks, Jami...

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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.


Asked: 2014-01-28 09:45:05 -0600

Seen: 3,655 times

Last updated: Apr 21 '14