I just want to make it clear.
I need to calculate FPKM. I use this formula: Normalized = [(raw_read_count)(10^9)] / [(gene_length)(XXXX)],
XXXX = the count of all reads that are aligned to protein-coding genes in that alignment.
How should I calculate XXXX? Is it just sum of all raw_read_counts after htseq-count (e.g. in R it will be XXXX <- sum(collumn_with_raw_red_counts)?