Question: ".1" being appended to Ensembl Gene IDs from UCSC txdb (dm6)
0
benformatics • 1.1k wrote:
When I get the genes (GenomicFeatures function) from a TxDb generated from UCSC using the following command:
txdb.ucsc <- makeTxDbFromUCSC("**dm3**","ensGene")
genes(txdb.ucsc)
All the names look like normal ensembl IDs.
FBgn0000003, FBgn0000008, FBgn0000014, etc..
When I switch to the newer Drosophila genome:
txdb.ucsc <- makeTxDbFromUCSC("**dm6**","ensGene")
genes(txdb.ucsc)
All the ensembl.ids have a ".1" appended to the end
All the names don't look like normal ensembl IDs.
FBgn0000003.1, FBgn0000008.1, FBgn0000014.1, etc..
Is there something I am missing here to avoid this? Other than this simple fix --> gsub("[.]1$","",names(x))
Even when I fix it, the names are still unique so its not a matter of duplicate names. My question then is really why is it even there...
ADD COMMENT
• link
•
modified 3.4 years ago
by
geek_y ♦ 9.8k
•
written
3.4 years ago by
benformatics • 1.1k