BioMart dataset for S pombe

Question

[cl10101]

I'm trying to download TxDB from BioMart for Schizosaccharomyces pombe using:

library(GenomicFeatures)
library(biomaRt)
makeTxDbFromBiomart(biomart ="fungal_mart" ,dataset="spombe_eg_gene" ,host="fungi.ensembl.org")

but I get error message:

Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... Error '.Ensembl_getMySQLCoreDir(dataset)':
  found 0 or more than 1 subdir for "spombe_eg_gene" dataset at ftp://ftp.ensembl.org/pub/current_mysql/

It seems that my host declaration is ignored. I've tried to specify full host address, but I can't find find information what is this full address.

If I use: biomaRt::useMart( biomart="fungal_mart",dataset="spombe_eg_gene", host="fungi.ensembl.org") it works and I get

"Object of class 'Mart':
 Using the fungal_mart BioMart database
 Using the spombe_eg_gene dataset" but I have no idea how to convert it to TxDB.

[Assa Yeroslaviz]

makeTxDbFromBiomart(biomart ="fungal_mart" ,dataset="spombe_eg_gene" ,host="fungi.ensembl.org")

This would work with the correct name

 makeTxDbFromBiomart(biomart ="fungi_mart" ,dataset="spombe_eg_gene" ,host="fungi.ensembl.org")

Answer 1

[Sentinel156]

Hi,

Did you find a solution to this? I was also having the same issue. There seems to be a problem pulling the metadata from the wrong host address as you say. I didn't want to waste time manually editing the makeTxDbFromBiomart() function so I made a TxDb from GFF3 file instead as follows:

link <- "ftp://ftp.ensemblgenomes.org/pub/release-34/fungi/gff3/schizosaccharomyces_pombe/Schizosaccharomyces_pombe.ASM294v2.34.gff3.gz" txdb <- makeTxDbFromGFF(link, format = "gff3", organism = "Schizosaccharomyces pombe", taxonomyId = "4896")

Making the TxDb this way has been fine for my ChIP-seq analysis, hopefully it works for you.