I am planning to use the --very-sensitive option for aligning my ATAC-seq reads. However, after reading the manual section below, I am unclear as to whether this option should be combined with --no-1mm-upfront or not?
"By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch end-to-end alignment for the read before trying the multiseed heuristic. Such alignments can be found very quickly, and many short read alignments have exact or near-exact end-to-end alignments. However, this can lead to unexpected alignments when the user also sets options governing the multiseed heuristic, like -L and -N."