Can someone please explain the what are RPKM and FPKM? And which one should I use and when?
RPKM: Reads Per Kilobase of transcript per Million mapped reads.
FPKM: Fragments Per Kilobase of transcript per Million mapped reads.
FPKM is very similar to RPKM. RPKM was made for single-end RNA-seq, where every read corresponded to a single fragment that was sequenced. FPKM was made for paired-end RNA-seq. With paired-end RNA-seq, two reads can correspond to a single fragment, or, if one read in the pair did not map, one read can correspond to a single fragment. The only difference between RPKM and FPKM is that FPKM takes into account that two reads can map to one fragment (and so it doesn’t count this fragment twice).