How to properly quantify gene expression of tandem duplicates from RNA-seq

Question

[missTique]

Reads that map to multiple locations are often penalized in most alignment and quantification pipelines. But tandem duplications of genes are common in many species. How can you properly align and quantify RNA-seq reads onto identical tandem duplicates?

[dthorbur]

Though I haven't looked, I'm sure some RNAseq tools will have ways to handle this. But to be sure, you could de-duplicate your transcriptome file prior to providing it as a reference. However, it should be noted that copy number variation of a given transcript can be polymorphic within and among populations, and this is seldom accounted for (at least I don't remember ever reading that).