Hello!
I am trying to use CLIPdb from the POSTAR3 site http://111.198.139.65/RBP.html , and have a couple questions.
I have bulk downloaded the RBP binding data for each of the 7 organisms in CLIPdb; I can see for each RBP, information such as peak start and end coordinates. Given that these are provided with genomic coordinates, I am wondering if there is an efficient way to distinguish between whether the target was pre-mRNA or mRNA? For instance, if the RBP has bound spliced mRNA, how would I distinguish that the binding site spans 2 adjacent exons with the intron removed from the case where intron is present?
Relatedly, there is a way within CLIPdb for me to input an RBP of interest, and output all the RBP’s target gene IDs. Information such as “target gene type” which is present here would be very useful to have as an additional column in the bulk download, or better yet, if I expand the “binding site records”, I can see a column that usually states whether the binding site is in an exon or intron. Is there a way for me to perform the bulk download (all RBPs) with these additional columns specifying target gene type and/or whether binding is in an exon or intron?
Greatly appreciative of your support!
