Question: ".1" being appended to Ensembl Gene IDs from UCSC txdb (dm6)
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gravatar for benformatics
3.4 years ago by
benformatics1.1k
ETH Zurich
benformatics1.1k 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...

R org.db ucsc biomart ensembl • 1.0k views
ADD COMMENTlink modified 3.4 years ago by geek_y9.8k • written 3.4 years ago by benformatics1.1k
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