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using alternate references??

asked 2013-07-29 13:16:44 -0700

Austin Meier gravatar image

Is it possible to load a reference sequence to use instead of the list given?

I work on potato, and I'd like to use this genome browser, but if I can't choose potato from the list of references, this program becomes fairly useless to me.

It seems like it'd be a simple thing to do, so maybe I'm just missing it somewhere. Thanks,

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answered 2014-04-21 11:20:08 -0700

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 2014-01-28 09:40:51 -0700

Olga Gonzalez gravatar image

Hi

I have the same problem, 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 2013-09-06 16:35:21 -0700

Hi Stephen,

I was able to put together the reference allele track and assembly file for the E. coli genome. I will email them both to you for testing. For GenomeBrowse to correctly identify a reference for a BAM file the assembly file needs to contain the correct "chromosome" names and lengths for the genome, for the E. coli bacteria I was unable to find a consistent listing for the name so in the assembly file I have listed all the possible ones I could find.

Let me know if you have any issues and we can do some editing to get it to work.

Thanks, Jami...

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answered 2013-08-22 11:08:25 -0700

Ok thanks Jami... it should be fairly straightforward..

cheers steve

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answered 2013-08-16 16:38:15 -0700

Hi Stephen,

We have never built IDF tracks for a bacteria genome before so I will need to take a look at the files that are available on the site to see if the data is provide in a format that can be easily used by our software.

I will let you know what I find out.

Thanks, Jami...

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answered 2013-08-15 08:19:01 -0700

Hi

I'm interested in using/testing this browser however I would like to have IDF tracks for these two genomes.. Having the ability for a user to upload their own reference is crucial...

ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/EscherichiacoliK12substr_MG1655uid57779/ ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/PseudomonasaeruginosaPAO1_uid57945/

thanks steve

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answered 2013-08-02 15:18:42 -0700

Hi Austin,

The most recent build (PGSC_DM_v3_2.1.11) of the Potato Genome is now available for use in GenomeBrowse.

You can download the necessary reference sequence tracks from the Annotations tab of the Add dialog.

I will email you a copy of the assembly file you will need to visualize your BAM files for this genome on the correct chromosome scale for your species.

Please let me know if you have any further questions.

Thanks, Jami...

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answered 2013-07-30 09:33:45 -0700

Dear Austin,

Currently GenomeBrowse will only accept reference sequence tracks that are in our IDF format. At the moment the tools within our analysis software SVS are the only available source for creating IDF files.

We are in the process of developing a tool for GenomeBrowse that will allow the user to import their own files to create these necessary tracks. In the case of reference sequences we will be allowing for direct import of FASTA files to create the IDF tracks necessary for computing coverage information for BAM files. The new functionality is schedule to be implemented by the end of September.

In the meantime I would be happy to create the necessary files for the Potato Genome and make them available for download through GenomeBrowse. The tracks should be complete by the end of the week and I will let you know when you can download them through GenomeBrowse.

Let me know if you have any questions.

Thanks, Jami...

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Asked: 2013-07-29 13:16:44 -0700

Seen: 634 times

Last updated: Apr 21 '14