bbmerge mismatched

[danova]

Hi,
While merging 16S pair-ended miseq data (2x250) i would like to disable ambiguous bases. BBmerge documentation states the following "When there is a mismatch, the base chosen is the one with the higher quality value, or N if they are equal". I have at most 1000 sequences in this case out 80000 that are assigned an "N" so i will like to remove those.

I´m just wondering if it is possible with bbmerge to discard reads that fall into this category so i don´t get ambiguous bases, neither i want to choose between one base or the other, simply discard merged reads with N.
Note that my R1 and R2 reads do not contain ambiguous bases as i have cleaned them before merging.

Thanks,

[westerman]

Why not discard the reads after merging. Using the BBTools 'reformat.sh' program the option 'maxns=0' should do what you want.

[Brian Bushnell]

Why not discard the reads after merging. Using the BBTools 'reformat.sh' program the option 'maxns=0' should do what you want.

+1

N's after merging are a special case, though, since they only encompass reads that had differing bases with the exact same quality value. If you want to be really strict, you could set "maxratio=0" to forbid any merges in which any bases differ. I'm not sure if that would ever be a good idea, though. To adjust stringency, I recommend using the presets "vloose, loose, default, strict, vstrict" which are more robust in my testing than modifying any individual variable.

[danova]

thanks for the tips