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#248 missing genes?
These genes no longer exist.
http://www.pombase.org/status/new-and-removed-genes
can you let me know where they are referred to?
Thanks
Val
skipping annotation: can't find feature for: SPAC1F12.03c
skipping annotation: can't find feature for: SPBC1348.13
As far as I can tell these do still exist, at least the ones I checked so far? (I think they are possibly all synonyms, arisen from merges?)
Val
skipping annotation: can't find feature for: SPNCRNA.817
skipping annotation: can't find feature for: SPNCRNA.77
skipping annotation: can't find feature for: SPNCRNA.78
skipping annotation: can't find feature for: SPNCRNA.193
skipping annotation: can't find feature for: SPNCRNA.75
skipping annotation: can't find feature for: SPNCRNA.884
skipping annotation: can't find feature for: SPNCRNA.18
skipping annotation: can't find feature for: SPNCRNA.951
skipping annotation: can't find feature for: SPNCRNA.958
skipping annotation: can't find feature for: SPNCRNA.994
skipping annotation: can't find feature for: SPNCRNA.101
skipping annotation: can't find feature for: SPNCRNA.1341
skipping annotation: can't find feature for: SPNCRNA.1347
skipping annotation: can't find feature for: SPNCRNA.104
skipping annotation: can't find feature for: SPNCRNA.1380
skipping annotation: can't find feature for: SPNCRNA.1388
skipping annotation: can't find feature for: SPNCRNA.1486
skipping annotation: can't find feature for: SPNCRNA.106
skipping annotation: can't find feature for: SPNCRNA.1612
skipping annotation: can't find feature for: SPNCRNA.1652
skipping annotation: can't find feature for: SPNCRNA.1679
skipping annotation: can't find feature for: SPNCRNA.1098
skipping annotation: can't find feature for: SPNCRNA.64
skipping annotation: can't find feature for: SPNCRNA.125
skipping annotation: can't find feature for: SPNCRNA.489
skipping annotation: can't find feature for: SPNCRNA.1196
skipping annotation: can't find feature for: SPNCRNA.582
skipping annotation: can't find feature for: SPNCRNA.502
skipping annotation: can't find feature for: SPNCRNA.10
skipping annotation: can't find feature for: SPNCRNA.1254
skipping annotation: can't find feature for: SPNCRNA.1274
skipping annotation: can't find feature for: SPNCRNA.1291
skipping annotation: can't find feature for: SPNCRNA.1295
and
skipping annotation: can't find feature for: SPBTRNAASP.03
http://www.pombase.org/search/ensembl/%20SPBTRNAASP.03
that flavor of message comes from loading the quantitative gene expression data
pombe-embl/external_data/Quantitative_gene_expression_data/
...and it does rather look like that loader isn't using gene/feature synonyms
OK that means if we map them to the new ID there will be duplicate gene expression data for these.....
Not sure what to do...
show both?
show one randomly?
ask Sam?
I vote we NOT do anything random. How about ask Sam, but in the meantime display the data for the primary ID (which is effectively what it does now)?
Yes lets carry on as normal for now. I already mailed Sam.
Yep, in most cases it only checks the systematic_id (uniquename in Chado) when loading. In some cases it checks the primary gene name too.
I can change it to use the synonyms as well if that's appropriate.
I think for now we should keep as is, as it alerted us to the fact that there are 2 lots of data for some genes.
In these issues we might need to handle on a case by case basis
we can discard the data for
skipping annotation:
can't find feature for: SPAC1F12.03c
skipping annotation: can't find feature for: SPBC1348.13
as these are now nUMT's not genes
will raise priority once Sam responds. No harm now if a few duplicate annotations exist