BioMart dataset for S pombe
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4.9 years ago
cl10101 ▴ 80

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
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.

biomart bioconductor s. pombe GenomicFeatures R • 1.9k views
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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")

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Entering edit mode
4.9 years ago
Sentinel156 ▴ 180

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.