Fig. 1

Number of sequences that are mapped by srnaMapper, but are not mapped exhaustively by other tools. The number of sequences that do not map is in blue (“missed”). Among the sequences that map, we provided the number of sequences that do not map with the minimum number of errors (e.g. a tool mapped a sequence with 2 errors, whereas a hit with 1 error exists) in green (“nonoptimal”). Among the sequences that map optimally, we provided the number of sequences such that hits were missed in magenta (“fewer hits”). These numbers are not provied for non-exhaustive recipes, which are expected to miss all but one hit for multi-mapping sequences. The “bowtie2.vs.mult” recipe was omitted from the H. sapiens benchmark, because the tool required more than one week to complete, with 10 threads. The left panel provides the results when soft clipped nucleotides are considered as errors. The right panel provides similar results for tools that implement soft clipping, when soft clipping is not considered as error. In this context, other tools may map more reads, with fewer errors, or at more locations than srnaMapper. We provided the number of such reads in negative y values