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Relative error of single end reads (red curves) and paired end reads (blue curves) with different settings of parameters: (a) 70bp reads, true isoform expression vector (0.5, 0.5) (b) 30bp reads, true isoform expression vector (0.1, 0.9) (c) 30 bp reads, true isoform expression vector (0.5, 0.5), exon lengths (500 bp, 200 bp, 500 bp). When compared with n (e.g., 5000) single end reads, n/2 (i.e., 2500) pairs of paired end reads were used.
