Table 3

Parameter values used in the first application example

Parameter

Value


Maximum number of mismatches at 5'-end

3


Maximum number of mismatches at 3'-end

3


Sequence range from the ends

46 bp


Continuous trimming

Yes


Remove sequences not matching tag sequence

No ("don't remove")


Minimum read length

50 bp


Maximum read length

Default (maximum length)


Threshold for occurrence of N

5%


Dereplicate data (remove exact sequence copies)

Yes


Fragment-to-fragment splitting

Yes


Maximum number of mismatches for splitting

3


Schmieder et al. BMC Bioinformatics 2010 11:341   doi:10.1186/1471-2105-11-341

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