I performed RNA-seq for a sample and want to calculate RPKM values. But I have two questions for your help.
1) Since paired-end Illumina sequencing was performed, can I use either single reads or fragments (i.e. paired reads) to calculate RPKM?
2) Let's suppose the total numbers of clean reads is A, among which the total number of mitochondrial reads is B. So, if I only want to calculate RPKM for mitochondrial genes, should I use A or B during calculation?
Thanks for any comments.