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)?


Thanks!
I've got answer from GDC portal:

> 1.  Download GTF files used in HTSeq analyses:  https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files (GDC.h38 GENCODE v22 GTF)
2. Extract only protein-coding gene IDs: less gencode.v22.annotation.gtf | grep "\tgene\t" | grep protein_coding | cut -f9 | cut -f2 -d '"' > EnsembleIDsPCG.txt
3. Use resulting list to extract only protein-coding values from counts file:  less CountFile.txt | grep -Ff ProteinCodingGeneList.txt > CountOnlyProt.txt 
4. Sum the values of "CountOnlyProt.txt" and that will give you your denominator value.

My problem was that I counted reads for all genes, but should only for protein-coding.

P.S. thanks to GDC support team!