bedtools merge only overlapping but not book-ended features

[Melina Klostermann]

Hello,

I am buildng a pipeline for iCLIP analyses, that should output single-nuclotide resolution, meaning every entry in the bed output should be only 1nt long. I would love to use the bedtools merge to sum up the score in the 1nt features, but not merge book-ended features. Is there a way to do that?

My command is

input.bed | bedtools merge -c 4 -o sum > output.bed

I tried to set -d -1 to exclude book-ended features, but that did not do it.

Many thanks in advance!

Bests,

Melina Klostermann