I have a data set of de novo assembled RNA-seq datasets across different sample types.
When BLASTing, many of the matches of the individual transcripts match to the same gene on the reference genome. However, each individual transcript has its own unique FPKM value.
I'm confused, firstly, as to how you can have multiple sequences from the same gene with different FPKM values — and of course, I'm also wondering what would be a suitable approach for the subsequent analysis. Should I just add the FPKM values together for the sequences with the same matches?