Dear friends,

I am a cookie in RNA-Seq analysis so I am really confused with the Ensembl id and gene symbol.  I have checked some associated posts in Biostars but I didn't find what I want eventually. The problem is that I noticed one Ensembl id matches multiple gene symbols, but I do not know how to deal with this issue when I want to do some analysis based on gene symbols. Should I add the counts of the same symbol together? Thanks in advance for the reply!
You have run into the problem that in the human genome there are instances of gene_names which are associated with multiple genomic loci (RF0019 in the link you posted). Since they are associated with different loci they also have different gene_ids. Last time I checked there were ~100 such gene_names in the human genome - many of which are located on different chromosomes.

I would always analyze the data with gene_ids (!) simply because else you assume the different loci produce identical products which might or might not be the case. Furthermore the gene_id analysis lets you analyze different things such as regulation and isoform switches. Lastly if you want to do any downstream analysis (go-terms or gene-set enrichment analysis etc) you should **NEVER** use gene_names. The problem is that in many cases gene_names are to unspecific with many different gene names pointing to the same gene and multiple genes all pointed to by a single gene name.

Cheers
Kristoffer