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converting gff files

asked 2015-02-10 17:52:11 -0600

When I try to convert a gff file to an annotation track, in the "Convert Data Source" window:

  • Genome Browser doesn't seem to directly recognize my .gff file extension
  • Once it reads the file in, it tells me to define the columns, but if I try to define them (for example as "Start Field" or "Stop Field", from the drop-down menu on each column), it immediately give me an error saying "The genomic Start field index no longer is valid"

Is that an error with my indexes somewhere?

thanks.

B

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answered 2015-04-27 09:04:28 -0600

Unfortunately the GenomeBrowse Convert Wizard does not support conversion of GFF files. Do your GFF files contain gene annotation data? The Convert Wizard is only able to handle GTF format for gene annotation sources or a more generalized text based format where each gene is a single line in the text file.

We have tools available in our analysis software, SVS, that can convert GFF files but since those tools are written in Python they are unable to be used in the stand-alone version of GenomeBrowse.

What type of data are you trying to convert? If the data type can be supported in GTF format you may want to covert the GFF data directly to GTF then you will be able to use the Convert Wizard to reformat the data for loading in GenomeBrowse.

Please let me know how I can help you further.

Thanks, Jami…

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Asked: 2015-02-10 17:52:11 -0600

Seen: 49 times

Last updated: Apr 27 '15