Figure 1

FPKM bias induced by coverage bias and transcript modifications. The points represent RefSeq isoforms and the plot shows the length dependency of the FPKM of the sequenced reads for input material where each isoform has the same abundance and where the isoforms exhibit coverage bias or transcript modifications, respectively. The nominal FPKM implied by the isoform abundance and the nominal isoform length is indicated as horizontal line. The fragmentation step in the library preparation generates fragments of an approximate length of 200 nt and causes the sharp peak of highly overestimated FPKM for isoforms having approximately this length.