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
These were the files availble for Oryza sativa: ftp://ftp.ensemblgenomes.org/pub/plants/release-37/gff3/oryza_sativa/
File: Oryza_sativa.IRGSP-1.0.37.gff3.gz
File: Oryza_sativa.IRGSP-1.0.37.chr.gff3.gz
File: Oryza_sativa.IRGSP-1.0.37.abinitio.gff3.gz
File: Oryza_sativa.IRGSP-1.0.37.chromosome.1.gff3.gz
File: Oryza_sativa.IRGSP-1.0.37.chromosome.3.gff3.gz
File: Oryza_sativa.IRGSP-1.0.37.chromosome.2.gff3.gz
File: Oryza_sativa.IRGSP-1.0.37.chromosome.4.gff3.gz
File: Oryza_sativa.IRGSP-1.0.37.chromosome.6.gff3.gz
File: Oryza_sativa.IRGSP-1.0.37.chromosome.5.gff3.gz
File: Oryza_sativa.IRGSP-1.0.37.chromosome.7.gff3.gz
File: Oryza_sativa.IRGSP-1.0.37.chromosome.8.gff3.gz
File: Oryza_sativa.IRGSP-1.0.37.chromosome.11.gff3.gz
File: Oryza_sativa.IRGSP-1.0.37.chromosome.12.gff3.gz
File: Oryza_sativa.IRGSP-1.0.37.chromosome.9.gff3.gz
File: Oryza_sativa.IRGSP-1.0.37.chromosome.10.gff3.gz
Should I use the first file or should I combine each chromosome files in some way before feeding it into makeTxDbfromGFF?
Hey,
Hey, I'm using deseq2 after kallisto to analyze rice data. I'm using an ensembl gtf and I want to create a txdb. I used this function:
txdb2 <- makeTxDbFromGFF(file="C:/Users/Dee/Desktop/Thesis_rice/Oryza_sativa.IRGSP-1.0.37.gtf", dataSource=paste("ftp://ftp.ensemblgenomes.org/pub/plants/release-37/gtf/oryza_sativa/",sep=""), organism="Oryza sativa")
and I got that error:
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Error in c(x, value) :
could not find symbol "recursive" in environment of the generic function
any help?
Might be a problem in the makeTxDbFromGFF function from the GenomicFeatures package. It works with the ensDbFromGtf from the ensembldb package.
> library(ensembldb)
> dbf <- ensDbFromGtf("Oryza_sativa.IRGSP-1.0.37.gtf.gz")
Importing GTF file ... OK
Processing metadata ... OK
Processing genes ...
Attribute availability:
o gene_id ... OK
o gene_name ... OK
o entrezid ... Nope
o gene_biotype ... OK
OK
Processing transcripts ...
Attribute availability:
o transcript_id ... OK
o gene_id ... OK
o transcript_biotype ... OK
OK
Processing exons ... OK
Processing chromosomes ... Fetch seqlengths from ensembl ... OK
Generating index ... OK
-------------
Verifying validity of the information in the database:
Checking transcripts ... OK
Checking exons ... OK
Warning messages:
1: call dbDisconnect() when finished working with a connection
2: In ensDbFromGRanges(GTF, outfile = outfile, path = path, organism = organism, :
I'm missing column(s): 'entrezid'. The corresponding database column(s) will be empty!
3: closing unused connection 7 (ftp://ftp.ensemblgenomes.org/pub/release-37/plants/mysql/)
4: closing unused connection 6 (ftp://ftp.ensemblgenomes.org/pub/release-37/metazoa/mysql/)
5: closing unused connection 5 (ftp://ftp.ensemblgenomes.org/pub/release-37/fungi/mysql/)
6: closing unused connection 4 (ftp://ftp.ensemblgenomes.org/pub/release-37/bacteria/mysql/)
7: closing unused connection 3 (ftp://ftp.ensembl.org/pub/release-37/mysql/)
> edb <- EnsDb(dbf)
> edb
EnsDb for Ensembl:
|Backend: SQLite
|Db type: EnsDb
|Type of Gene ID: Ensembl Gene ID
|Supporting package: ensembldb
|Db created by: ensembldb package from Bioconductor
|script_version: 0.0.1
|Creation time: Sat Nov 25 18:53:08 2017
|ensembl_version: 37
|ensembl_host: unknown
|Organism: Oryza_sativa
|genome_build: IRGSP-1.0
|DBSCHEMAVERSION: 1.0
|source_file: Oryza_sativa.IRGSP-1.0.37.gtf.gz
| No. of genes: 91992.
| No. of transcripts: 98663.
>
cheers, jo
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version 2.3.6
Hello,
This worked! thank you :) If you post your answer as a top level comment I can accept it.
Also
library(GenomicFeatures)should be there formakeTxDbFromBiomart()to work.Done. I added the
library(GenomicFeatures)line. Thanks for the feedback!Cheers,
H.