I am using VEP to annotate a VCF and I am getting some results in the
MOTIF_NAME field, which indicates if the variant occurs in a region containing a TF binding site.
But, those motif names are not beign recognised by Ensembl.
As an example those are some of the
MOTIF_NAME values that I get:
Do you know where can I find the name of the factors corresponding to this binding sites?
It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/13460/where-to-find-ensembl-tfbs-names
This is typically not recommended as it runs the risk of annoying people in both communities.
Maybe this here helps: http://www.ensembl.info/2018/10/03/ensembl-94-is-out/
I ahven't used VEP is a while, check if this export option exists.
@ATpoint Thanks for your answer, but I've been checking VEP custom annotation and I think this is not what I am shearching. VEP is already returning the MOTIF_ID that exist in some of the coordinates where I found variants. The problem is that, this ID, which I think is in Ensembl format is not being recognised by Ensembl. And I don't know how to get this Motif name.
I cannot build a custom database of this names because this is precisely what I am looking for. Do you know where I could find the database from which VEP is geting this motif names? I was being looking in cache dir, but it is complex to find it there.
Hi, Im having the same issue. Have you found a solution to search for those motif based on VEP motif (ENSM..........). ?