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I am using an archived version of the Ensembl mart for mm9 mouse genome and the following code: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',
where gene.names is a list of ensembl gene ids.
Thank you very much in advance!