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Old 02-24-2012, 02:48 AM   #3
kenphi
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Location: Heidelberg, Germany

Join Date: Nov 2009
Posts: 2
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Dear silin

I think this is because in your reference annotation there are "unrelated" transcripts annotated to the same gene. I noticed that this happens, when there are independent transcript groups, i.e. groups of transcripts that do not overlap in exon coordinates. The can be side-by-side or one in the intron of the other. Some examples are in Ensembl 64

ENSMUSG00000086255
ENSMUSG00000062352
ENSMUSG00000021879
ENSMUSG00000033705
ENSMUSG00000087461
ENSMUSG00000022105
ENSMUSG00000073791
ENSMUSG00000052675
ENSMUSG00000055407
ENSMUSG00000056856
ENSMUSG00000027203

In some of these cases, I would say that Ensembl didn't follow its own guidelines, to assign the same gene identifier to transcripts with overlapping position, because there are clearly independent clusters.

I keep them and use the gene_id column of cufflinks to make tables unique.

Philip
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