why do I get error for building txdb for S. pombe from biomart?

Question

[Parham]

Hi,

I get an error while making txdb from biomart for S. pombe. Can someone tell what am I doing wrong? It works when I give biomart="fungal_mart" . I am not sure if the txdb will be different?! Thanks . . .

txdb<-makeTranscriptDbFromBiomart(biomart ="fungi_mart_23" ,dataset="spombe_eg_gene" ,host="fungi.ensembl.org")
Error in useMart(biomart = biomart, dataset = dataset, host = host, port = port) : 
  Incorrect BioMart name, use the listMarts function to see which BioMart databases are available

[komal.rathi]

Did you try without providing the hostname:

makeTranscriptDbFromBiomart(biomart = "fungi_mart_23", dataset = "spombe_eg_gene")

[Parham]

Thanks. Will there be any difference in txdbs made in these two different ways. I mean fungal_mart vs fungi_mart_23 ? I am not bioinformatcian that's why I don't know how these databases are.

Answer 1

[Neilfws]

The error message tells you the problem. The mart fungi_mart_23 is not associated with the host fungi.ensembl.org.

listMarts(host = "fungi.ensembl.org")

            biomart               version
1       fungal_mart           Fungal Mart
2 fungal_variations Fungal Variation Mart

If you do not specify a host, the default is www.biomart.org, which does contain fungi_mart_23.

mart <- listMarts()
mart[grep("fungi", mart$biomart),]

              biomart                             version
5       fungi_mart_23           ENSEMBL FUNGI 23 (EBI UK)
6 fungi_variations_23 ENSEMBL FUNGI VARIATION 23 (EBI UK)