Reference sequence for amplicon mapping

Question

[omar-pons]

Hello, I've seen in the literature that when amplicons are sequenced by Illumina, the reads are always mapped against the whole genome, but I don't understand why it's not convenient to map the reads against the amplified region. Help please.

Answer 1

[lieven.sterck]

It would say it's simply to not bias the mapping from the start. If you have the (whole) genome at your disposal why then not use it? It will in one ago also give a control that you really amplified and sequenced what you expected.