Question: Xenopus tropicalis Ensembl Gene IDs and Transcripts ID with BiomaRt
0
gravatar for gaby_santos
3.4 years ago by
gaby_santos10
gaby_santos10 wrote:

Hi!

I am trying to retrieve all ensembl gene and transcripts IDs of Xenopus tropicalis using the biomaRt library.

getBM(attributes = c('ensembl_transcript_id', 'ensembl_gene_id'), filters ="chromosome_name", values="?", mart=ensembl)

Specifically I have doubt in the values parameter , as I do not know the scaffolds nomenclature to retrieve all the genes and transcripts using the chromosome name as filter.

Thanks!

Gaby

ensembl biomart R • 1.2k views
ADD COMMENTlink modified 3.4 years ago by Mike Smith1.5k • written 3.4 years ago by gaby_santos10
2
gravatar for Mike Smith
3.4 years ago by
Mike Smith1.5k
EMBL Heidelberg / de.NBI
Mike Smith1.5k wrote:

If you want to get all values for the attributes you're interested in, you don't need to supply any filters or values. The following query should return all available data, but bear in mind it might take a long time to run.

library(biomaRt)
ensembl <- useMart('ensembl', 
                   dataset = 'xtropicalis_gene_ensembl',
                   host = "www.ensembl.org")

transAndGene <- getBM(attributes = c('ensembl_transcript_id', 'ensembl_gene_id'), 
                      mart = ensembl)

We can look at the number of rows in transAndGene to see how many transcripts were returned.

> nrow(transAndGene)
[1] 24197

You can check this against the Ensembl annotation overview page here and see that it's the same number as listed there, so our query returned everything available.

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Mike Smith1.5k

how can i use this "transAndGene" to map my gene after I get result from deseq2 .I want to convert all the ENSEMBL to gene name can you let me know how do I do that?

ADD REPLYlink written 3.4 years ago by krushnach80830
1
gravatar for Emily_Ensembl
3.4 years ago by
Emily_Ensembl21k
EMBL-EBI
Emily_Ensembl21k wrote:

For values you should put in whichever chromosome you want to filter by. What chromosome are you looking to get the genes from?

ADD COMMENTlink written 3.4 years ago by Emily_Ensembl21k
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