Question: Obtaining promoter sequences with biomaRt R package
0
gravatar for ilyco
4.7 years ago by
ilyco50
United Kingdom
ilyco50 wrote:

Hello,

I tried to obtain the promoter sequences of 22 genes (2000 bp upstream) using the biomaRt R package and their Ensembl Gene Ids. However, the getBM() function returns 'Sequence Unavailable' for 20 of the genes and only retrieves the sequences for 2 of the genes. Do you know why this is happening and what alternatives do I have for obtaining the sequences?

I am using an archived version of the Ensembl mart for mm9 mouse genome and the following code:

promoters <- getSequence(id = gene.names, type='ensembl_gene_id',seqType='coding_gene_flank',
                                         upstream=2000,mart=ensembl67)

where gene.names is a list of ensembl gene ids.

Thank you very much in advance!

 

promoter sequence biomart • 2.8k views
ADD COMMENTlink written 4.7 years ago by ilyco50

Is this true when you use biomart web instead biomaRt ?

ADD REPLYlink written 4.7 years ago by poisonAlien2.7k

Thank you!

I downloaded all the upstream sequences of all the genes from biomaRt and selected the genes I wanted afterwards using the Ensembl Ids.

 

ADD REPLYlink written 4.7 years ago by ilyco50
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