I want to know the copy number of all ORFs in my genome. Does it make sense to map genomic reads to these ORFs using either BWA or Bowtie, and then quantify FPKM values with cufflinks?
I expect most ORFs are in 1 copy, so they will have about the same FPKM. I can then normalize all FPKM values to the value corresponding to a single copy ORF, and see how many copies other ORFs have.
Does this make sense? Any pitfalls? should I use bwa or bowtie for this?
Thank you for your advice, Adrian