Geneset Enrichment Analysis With Refseqid

Question

[k.nirmalraman]

I have RNA Seq data from a protocol that particularly enriches and sequences the 3' end of the mRNA. The sequences are aligned using transcriptome in bowtie. The count data of each refseqID is available for further analysis. However, I would like to do a Gene Set variance and enrichment analysis and I am stuck with the problem of multiple refseqID mapping to same gene symbol.

How can one address this issue when performing GeneSet enrichment analysis or the like? More particularly how to handle to corresponding read counts...

Any help me would be very much appreciated. Thanks!