Hi Keith,

Are you using a full BED12 file? Or just a BED3-6? Full BED12 should return the available features:


3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".

If you would like to share a history, that would help if this is not enough information ("Options -> Share or Publish). You can send the link to me directly.

Best,

Jen
Galaxy team

On 4/7/11 10:46 AM, Keith Giles wrote:
I am trying to use the galaxy "BED to GFF" function.  The operation
worked, but instead of giving me back any feature information (e.g.,
exon, intron, repeat, etc.); I just received back the sequence of the
interval contained within the BED file.  Does anyone know what I'm doing
wrong?  Moreover, does anyone know the best way to map each read of a
RNAseq run to a given feature?



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