-1
$\begingroup$

I'd like to perform a motif analysis of all promoter regions of the gene ENSMUSG00000020538 in mus musculus. To do so, I wanted to use Biomart :

library('biomaRt')
mart <- useMart("ensembl")
mart <- useDataset("mmusculus_gene_ensembl", mart = mart)
all.genes <- getSequence(id = 'ENSMUSG00000020538', 
                         type="ensembl_gene_id",
                         seqType="coding_gene_flank",
                         upstream=100, 
                         mart=mart)

But this provide me only the flanking region of the sepcified gene, not all its promoter regions. How could I do ?

$\endgroup$
0
0
$\begingroup$

Answer from @ATpoint, converted from comment:

You need to extract the TSS of all transcripts of that gene, not the gene borders. Query biomaRt for that gene, then set options to extract all transcripts, then get the sequence for the TSS coordinates of those (with a window).

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.