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Figure 3 | Genome Medicine

Figure 3

From: HLA typing from RNA-Seq sequence reads

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

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