I am working on a CUT & RUN library for the first time. The methods state: "Dovetail alignment policy. Bowtie210 aligns each mate of a pair separately and then discards any pairs that have been aligned inconsistently. Dovetail refers to the situation when mates extend past each other. In the default setting, these alignments are discarded. Dovetail is unusual but encountered in CUT&RUN experiments. The --dove-tail setting10 was enabled to flag this situation as normal or “concordant” instead of elimination of such reads."
But, when I checked my version of bowtie2 it seems that the default includes inconsistent pairs and that the only dove-tail option is " --no-dovetail not concordant when mates extend past each other" So... do I run bowtie2 as is?
Thanks in advance,