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Such biases can have adverse effects on both mapping rate and accuracy.
RRBSMAP shows the highest mapping rate and accuracy, with the similar speed as BSSEEKER.
Interestingly, for BS-seeker2, both mapping rate and mapping accuracy did not decreased substantially.
For all three mappers, the mapping rate and mapping accuracy fluctuated with changes in read quality.
Unsurprisingly, with increasing read length, mapping rate and accuracy increased and false-positive rates decreased.
However, Bismark tended to lose both mapping rate and accuracy when read error rate was higher in longer reads.
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We first examine overall mapping rates and locations of the four methods, illustrated in Figure 1.
For each of these methods, we explore mapping rates and locations, number of detected genes, correlations between computed expression values, and the utility of the resulting data for differential expression analysis.
The genome map rate and gene map rate were very low (lower than 7%) because, even though strawberry and blackberry belong to the family Rosaceae, they are quite distinct species and the alignment using the SOAP software was very strict (no more than 5 mismatches were allowed in the alignment) (Table 3).
This is based on the observation that read-mapping rate and detection accuracy of methylation levels are correlated.
Read mapping rate, duplication rate, and genome coverage without duplicate reads were determined and recorded for each sample (Additional file 1).
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