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It is important to keep reads with multiple matches in the genome, since they may map to real microRNAs.
As a compromise between the conflicting interests of accuracy of mapping and retaining information, we chose to keep reads with up to five equally good matches.
Assuming that the fragment length follows a normal distribution (Hormozdiari et al., 2009), we only keep reads with fragment length within three standard deviations from the mean.
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