Hi @Dr.Lida
For SE data RPKM should be identical to FPKM (a read is equal to a fragment).
It is a little bit complicated for PE data. If both F and R reads are mapped to a gene, the reads are counted as one fragment. Then there are complicated cases, for example, when only one read is mapped, or reads are mapped to different genes or not properly paired, e.g., mapped to different chromosomes. If only one read from a pair is mapped, usually the read corresponds to a fragment. I don’t know how not properly paired reads are treated.
Hope this helps.
Kind regards,
Igor
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