Best way to detect long insertions in bisulfite sequencing data?
You'd be best off by starting with -rfg and -rdg as is and reverting bismark's change of --score-min back to the default for bowtie2. That alone will allow for much longer indels. If that still doesn't suffice, then I'd play around more with --score-min before messing with the gap open/extend penalties. If you do need to play with those, then increase the gap open penalty and decrease the gap extension to 1. Do check that the resulting alignments aren't nonsense though!