I am looking for way to get sequences of 3'UTRs for entire transcriptomes, for a few dozen species.
I have tried doing this via biomart, but was unable to find this data in the FTP and downloading the data for so many species manually is unfeasible.
I have also tried to get the data via R biomaRt package, using the following code:
But the out indicated "Sequence unavailable" for about 95% of the genes. On the other hand, when I tried the same with a subset of 100 mouse genes, I received more then a 100 matches, with multiple non duplicated sequence matching a single Ensembl gene.
What would be the right approach to accomplish this task?
Thanks in advance