We're analyzing RNAseq data with a pipeline consisting of Salmon, tximeta, and DESeq2.
We have a multi-factorial experimental design, and the experiment was performed on cell lines.
On thing that surprised us is that in the result output, we observe many gene polymorphisms.
For example, for gene NLRP2 we observed multiple entries associated with different ensembl IDs ENSG00000022556, ENSG00000275082, ENSG00000275843, etc.
My question is how do we interpret data like this? And how to deal with this kind of situation? Can we add/average different entries associated with the same gene?