How to analyze RNA Targeted (Gene Panel) Ampliseq data?

Question

[Raito92]

Good evening to anyone, I'm about to get the results of my experiment. A panel of selected genes of insterest (250) have been successfully analyzed through different tissues by using a RNA Targeted approach, provided by Illumina Ampliseq. I don't have any of the default tools suggested on the website (MiSeq Report Tools)

I guess my data will consist of reads to analyze and not come in form of already 'quantified' reads.

How would you analyze this particular kind of data?

After removing adapters and quality filtering...

• Align to a reference genome or just to the list of RNA Targeted genes? If so, with which tool or script?
• What to use downstream to compare expression levels and perform DE analysis? edgeR or DESEQ2, which of them would work better in my case?

Any experience here?

Thanks in advance!