{quote}I was looking at the expression matrix CVS files for beta2 and
noticed that the GENCODE gene ids don't include the version number.
So they have lines like:
ENSG00000252830,5S_rRNA,rRNA,chr1,143439605,143439714,True
It would be far better if ENSG00000252830 included the version
number: ENSG00000252830.2.
While technically you can take the gencode release and look up
the version number, this is both extra work and the gencode
release often gets lost when results make it out in the wild.
I have seen this a lot with the UCSC browser dropping the refseq
version from the accession.
So I am trying to find out where the version number gets dropped
and get a policy establish to not do keep the version. Any idea
if this is happening at the analysis level?
My other job is GENCODE, so if you have information, I am the go-to guy.
From Mark Diekhan’s with HCA at UCSC:
{quote}I was looking at the expression matrix CVS files for beta2 and noticed that the GENCODE gene ids don't include the version number.
So they have lines like: ENSG00000252830,5S_rRNA,rRNA,chr1,143439605,143439714,True
It would be far better if ENSG00000252830 included the version number: ENSG00000252830.2.
While technically you can take the gencode release and look up the version number, this is both extra work and the gencode release often gets lost when results make it out in the wild. I have seen this a lot with the UCSC browser dropping the refseq version from the accession.
So I am trying to find out where the version number gets dropped and get a policy establish to not do keep the version. Any idea if this is happening at the analysis level?
My other job is GENCODE, so if you have information, I am the go-to guy.
{quote}
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