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Adding new genome assemblies

asked 2015-10-13 07:38:32 -0600

Sagi Polani gravatar image

Hi,

I would like to add to my GenomeBrowse a new assembly, including the fasta reference and matching annotations.

The genome of interest:

Staphylococcus aureus RF122

http://bacteria.ensembl.org/staphyloc...aureusrf122/Info/Index

I have downloaded the fasta reference file and matching gff3 annotation file, but when Genomebrowse doesn't seem to handle gff3 files. In this respect, I attempted to convert the gff3 file to gtf format using cufflinks' gffread, but when I attempt to convert the files together, I get a "The fields or type of this source does not match...".

Is there a simple way to get around this or import a genome (including the annotation data) directly from ensembl?

Thanks!

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answered 2016-03-11 16:34:58 -0600

Hi Sagi,

I wanted to let you know that we have added support for the Staphylococcus aureus RF122 genome.

You can download the Reference Sequence and Gene tracks by going to File > Add and selecting them from the Public Annotations location.

Let me know if you have any issues or questions about the new annotation sources.

Thanks, Jami...

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answered 2015-10-15 14:46:15 -0600

Hi Sagi,

I am sorry you are having issues adding your genome of interest to GenomeBrowse.

Unfortunately the stand-alone version of the software does not directly support converting gene annotations in GFF3 format. As you have seen we only support the GTF format that is based off the specifications determined by Washington State University in St. Louis (http://mblab.wustl.edu/GTF22.html).

If you can provide a sample of your converted GTF file I would be happy to take a look to see why the Convert Wizard is having issues.

I will also add this genome to the list of genomes to directly support through GenomeBrowse. It usually take a few weeks for them to be added and I will let you know when it can be downloaded from our Public Annotations.

Let me know if you have any questions.

Thanks, Jami...

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Asked: 2015-10-13 07:38:32 -0600

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Last updated: Mar 11 '16