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