Hi Karin,
I'd recommend using GFF3 as it's actively supported. You can get
information on the GFF3 spec at:
http://www.sequenceontology.org/gff3.shtml
If you have issues with the GFF3 files, please let us know.
Cheers,
Ed
On Mon, 10 May 2010, Karin Lagesen wrote:
Hi!
I am trying to figure out what goes where when I load a gff3 or ensembl
gff formated file. I see that the information from those files are
displayed in the bottom-most windows (as well as being used to draw the
genes, of course). However, I am uncertain where the information from each
column goes, and whether this varies according to what the source is. For
instance, in a gff ensembl formatted file I have (amongst others) the
following lines:
STAT_bind1 GeneWise cds 232019 232107 0.00 + 0
GeneScaffold_1701-genewise-prediction-1
STAT_bind1 GeneWise cds 232219 232279 0.00 + 1
GeneScaffold_1701-genewise-prediction-1
STAT_bind2 GeneWise cds 232538 232633 0.00 + 0
GeneScaffold_1701-genewise-prediction-2
STAT_bind2 GeneWise cds 232732 232779 0.00 + 0
GeneScaffold_1701-genewise-prediction-2
STAT_bind2 GeneWise cds 235325 235408 0.00 + 0
GeneScaffold_1701-genewise-prediction-2
90107 WGA2Genes similarity 167067 167276 0.0 + .
ENSGACP00000011294 41 110
90112 WGA2Genes similarity 173628 173771 0.0 + .
ENSGACP00000011294 112 159
90116 WGA2Genes similarity 174150 174275 0.0 + .
ENSGACP00000011294 160 201
75089 combined__ensembl exon 91409 91415 0.0 + .
5772
75092 combined__ensembl exon 91421 91614 0.0 + .
5772
75095 combined__ensembl exon 92106 92196 0.0 + .
5772
75097 combined__ensembl exon 92362 92495 0.0 + .
5772
75099 combined__ensembl exon 92735 92798 0.0 + .
5772
75101 combined__ensembl exon 92917 93104 0.0 + .
5772
So, here I have cdses, exons and similarities. Now, when I look at these
in apollo and click on one of those that are from GeneWise, I get as a
heading in the bottom right window STAT_bind2. A similar thing happens for
the combined_ensembl genes, where the heading for some reason becomes one
of the rightmost columns for the combined__ensembl. This does not happen
for the WGA2Genes, where I don't get the same kind of heading in the
bottom right window. In this case I just get WGA2Genes.
So, basically, is there any where I can get a detailed breakdown of what
the information that is found in a gff3 and/or ensembl gff formatted file
can be refound/used for in apollo?
Thanks!
Karin
--
Karin Lagesen, PhD
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