Table 1.
End-to-end | Local | ||||||||
---|---|---|---|---|---|---|---|---|---|
RCA | RCE | RCA | RCE | ||||||
Read length | Mean | SD | Mean | SD | Mean | SD | Mean | SD | |
Unpaired | 50 | −9.03 | 0.26 | −24.61 | 0.19 | −2.49 | 0.47 | −15.30 | 0.57 |
100 | −7.43 | 1.82 | −18.53 | 2.61 | −10.26 | 1.52 | −27.87 | 1.59 | |
150 | −9.11 | 1.15 | −16.22 | 0.62 | −14.77 | 2.15 | −29.27 | 1.03 | |
250 | −16.82 | 2.01 | −19.97 | 0.44 | −22.51 | 1.77 | −28.85 | 0.62 | |
500 | −33.77 | 0.60 | −27.26 | 0.37 | −37.75 | 1.32 | −31.65 | 1.01 | |
Paired | 50 | −13.11 | 0.44 | −19.60 | 0.44 | −18.60 | 0.28 | −33.63 | 0.24 |
100 | −15.80 | 1.29 | −21.79 | 0.33 | −36.84 | 0.69 | −45.42 | 0.53 | |
150 | −22.39 | 1.74 | −25.94 | 0.28 | −46.87 | 0.54 | −52.76 | 0.56 | |
250 | −37.65 | 0.97 | −33.48 | 0.22 | −58.39 | 0.91 | −58.75 | 1.38 | |
500 | −54.59 | 0.58 | −44.91 | 0.34 | −68.54 | 0.95 | −70.37 | 3.45 |
Relative change is expressed as a percentage. Each sample consists of 4 million reads/pairs. Samples are either unpaired or paired-end, and Bowtie 2 is run in either end-to-end or local alignment mode as indicated. Results are means and standard deviations over ten random trials, repeated starting from the input modeling step
CID cumulative incorrect difference
RCA relative change in area under CID
RCE relative change in sum of squared errors
SD standard deviation