I have been following the workflow available at [Importing transcript abundance datasets with tximport](http://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html) and it is required to use a TxDb object. I am working with Rice and there isn't a TxDb object for rice. But rice has a BSgenome object.

Is there any way I can use the BSgenome object? I just want to use my Salmon output to be used in DESeq2.

Hi,

Alternatively, you can use makeTxDbFromBiomart() to make a TxDb object from the Ensembl Plants mart:

library(biomaRt)
mart <- useMart(biomart="plants_mart", host="plants.ensembl.org")
datasets <- listDatasets(mart)
datasets[1:6 , 1:2]
#                dataset                               description
# 1    atauschii_eg_gene              Aegilops tauschii genes (...
# 2 obrachyantha_eg_gene Oryza brachyantha genes (Oryza_brachya...
# 3 ptrichocarpa_eg_gene                Populus trichocarpa gen...
# 4     ppersica_eg_gene                   Prunus persica genes...
# 5   stuberosum_eg_gene              Solanum tuberosum genes (...
# 6     sitalica_eg_gene                   Setaria italica gene...
idx <- grep("oryza", datasets$description, ignore.case=TRUE)
datasets[idx, 1:2]
#                    dataset                           description
# 2     obrachyantha_eg_gene  Oryza brachyantha genes (Oryza_br...
# 8          onivara_eg_gene                  Oryza nivara gene...
# 14       opunctata_eg_gene                Oryza punctata gene...
# 15         oindica_eg_gene               Oryza sativa Indica ...
# 18   oglumaepatula_eg_gene            Oryza glumaepatula gene...
# 19        obarthii_eg_gene                 Oryza barthii gene...
# 20         osativa_eg_gene            Oryza sativa Japonica g...
# 25   omeridionalis_eg_gene Oryza meridionalis genes (Oryza_me...
# 28      orufipogon_eg_gene                   Oryza rufipogon ...
# 38 olongistaminata_eg_gene Oryza longistaminata genes (O_long...
# 41     oglaberrima_eg_gene                    Oryza glaberrim...

Choose your dataset of interest (e.g. osativa_eg_gene), then:

library(GenomicFeatures)
txdb <- makeTxDbFromBiomart(biomart="plants_mart",
                            dataset="osativa_eg_gene",
                            host="plants.ensembl.org")

Please note that some important tweaks were made to makeTxDbFromBiomart() last week to improve its support for EnsemblGenomes (see here A: Errors with makeTxDbFromBiomart for the details) so make sure you use the latest version of GenomicFeatures (1.28.5) before trying the above.

Cheers,

H.

Ensemblgenomes provides gene models for many plants. Check http://plants.ensembl.org/index.html . You could either download a gtf or gff3 file for rice from there and build a TxDb using makeTxDbFromGff (GenomicFeatures package) or, since the data is in Ensembl format, an EnsDb using ensDbFromGtf (ensembldb package - EnsDb and TxDb packages/databases provide the same functionality/annotations).

For EnsDb, creating an EnsDb from a GTF you might lack some annotations since they are not provided in the file. If you tell me what release and species (which of the many oryza forms e.g. oryza_sativa, oryza_meridionalis etc) you'd need, I could build the EnsDb database/package for you directly from the ensemblgenomes MySQL databases - just let me know.

cheers, jo