Question: TxDb.Mmusculus.UCSC.mm9.knownGene showing exons with gene_id but there is no such gene
gravatar for tonja.r
3.5 years ago by
tonja.r450 wrote:

I have found some strange thing in this dataset. Namely, I have exons that correspond to one gene_id, but there is no gene with such gene_id in a dataset.

mm9 = TxDb.Mmusculus.UCSC.mm9.knownGene

exon dataset has a gene with ID 100038977

exon = exons(mm9)
gene_id_exons = select(mm9, keys=as.character(exon$exon_id), columns = c("GENEID"), keytype = "EXONID")
> gene_id_exons[which(gene_id_exons$GENEID == "100038977"),][1:4,]
243122 241618 100038977
243123 241619 100038977
243124 241620 100038977
243125 241621 100038977

gene dataset does not have a gene with such ID

> which(gene$gene_id == "100038977")

Why are there exons that belong to the 100038977 gene (Gm1993) but there is no such gene listed in the gene dataset?


The same happens with gene_ids 100039550 (Gm10486),100039890 (Gm15093),100039939 (Gm2506), 100040048 (Ccl27b), 100040631 etc


R • 1.1k views
ADD COMMENTlink written 3.5 years ago by tonja.r450

You might want to post this on the bioconductor support forum. I expect that the various Txdb packages are constructed with a script...perhaps it has a bug.

ADD REPLYlink written 3.4 years ago by Devon Ryan88k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2036 users visited in the last hour