Figure 3

Sensitivity versus specificity for different mapping and technical parameters applied to the 50 Montgomery test samples. Bowtie mapping parameters include -a (report all mappings), -m1 (report only unique mappings), -v<0|1|2> (allow zero, one or two mismatches), using the initial reference dataset consisting of exons 1 to 3, plus 75 nucleotides of exon 4. Analysis of different technical parameters comprised varying the average number of reads per sample (1e⁶, 5e⁶ and 10e⁶) while mapping against the initial reference dataset with '-a -v1', shortening the read length (from 73 nucleotides to 30 nucleotides) and using only one of the read pairs to simulate a single-end read dataset. nt, nucleotide; PE, paired-end; SE, single-end