Question

tximport using Ensembdb to create Tx2gene dataframe with bovine transcripts ?

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gilles.charpigny • 0

@gillescharpigny-16618

Last seen 5.7 years ago

I used Salmon to quantify my RNA-seq. As proposed in the Salmon tutorial I downloaded and indexed a bovine transcriptome from Ensembl (ftp.ensembl.org/pub/release-93/fasta/bos_taurus/cdna/Bos_taurus.UMD3.1.cdna.all.fa.gz) After quantification, i plan to use tximport package to aggregate transcrits to the gene level for gene-level differential expression analysis in order to continue analysis using DESeq2. In the tximport vignette it is proposed to create a tx2gene dataframe by using ensembldb package. The recommendations of the tutorial are as follows: if you are using an Ensembl transcriptome, the easiest way to create the tx2gene data.frame is to use the ensembldb packages. The annotation packages can be found by version number, and use the pattern EnsDb.Hsapiens.vXX. The exemple is for human data.

My question is:

how to do in bovine species knowing that I indexed on a bovine cdna database from Ensembl. Where can I find any annotation package for the bovine species and a pattern like EnsDb.Btaurus.vXX?

Thank you very much for your help

GCH

tximport ensembldb bos taurus tx2gene • 2.5k views

ADD COMMENT • link updated 6.3 years ago by James W. MacDonald 67k • written 6.3 years ago by gilles.charpigny • 0

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Hi Gilles

you can use the following packages :

- AnnotationDbi

-Annotate

-Ensembldb

-Biomart

Here are the following code I used for using Bovine Ensembl DB for differential expression analysis

ensembl_mart_93 <- useEnsembl(biomart="ensembl")# to use the latest ENSEMBL version

mart= useMart('ensembl') # connecting to ENSEMBL
listDatasets(mart)# List of the available datasets

mart<-useMart(biomart="ensembl", dataset="btaurus_gene_ensembl", host="www.ensembl.org",
path="/biomart/martservice", verbose = FALSE) # use of Bos taurus dataset.

Regards

Carine

ADD REPLY • link 6.3 years ago cagenet34 ▴ 20

score 1 · Answer 1 · 2018-07-31

I have no idea what you mean by

how to do in bovine species knowing that I indexed on a bovine cdna database from Ensembl

will you clarify? As for the second question:

> library(AnnotationHub)

> hub <- AnnotationHub()
updating metadata: retrieving 1 resource
  |======================================================================| 100%

snapshotDate(): 2018-04-30
> query(hub, c("taurus","ensdb"))
AnnotationHub with 6 records
# snapshotDate(): 2018-04-30
# $dataprovider: Ensembl
# $species: Bos Taurus
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH53189"]]'

            title                          
  AH53189 | Ensembl 87 EnsDb for Bos Taurus
  AH53693 | Ensembl 88 EnsDb for Bos Taurus
  AH56658 | Ensembl 89 EnsDb for Bos Taurus
  AH57731 | Ensembl 90 EnsDb for Bos Taurus
  AH60745 | Ensembl 91 EnsDb for Bos Taurus
  AH60948 | Ensembl 92 EnsDb for Bos Taurus
> btens <- hub[["AH60948"]]
require("ensembldb")
downloading 1 resources
retrieving 1 resource
  |======================================================================| 100%

loading from cache
    'C:/Users/jmacdon/AppData/Roaming/AppData/.AnnotationHub/67694'
> btens
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: 0.3.2
|Creation time: Sun Apr  8 11:33:37 2018
|ensembl_version: 92
|ensembl_host: localhost
|Organism: bos_taurus
|taxonomy_id: 9913
|genome_build: UMD3.1
|DBSCHEMAVERSION: 2.1
| No. of genes: 24616.
| No. of transcripts: 26740.
|Protein data available.
>