Hi folks!

I have two GFF3 files, one with annotated genes. Another with predicted transposons.

I want to find the numerical distribution of the distances between transposons and genes.

I already found the distance amongst just transposons, and amongst just genes - using the 'spacing' sub-command of bedtools 2.2.4.0, however 'spacing' cannot compare two GFF files.

For comparing spacing of features in 2 separate GFFs, bedtools 2.24.0 has the reldist sub-command, but this does **not** yield absolute distance in base pairs, but only relative distance distribution, so its not so useful to me...

So I am not sure if there is an off the shelf option in bedtools that can help me answer this question. Would any of you have a simple solution to my problem? It does not have to be using bedtools... Thank you!
Maybe `closestBed` with `-d` option is what you want?

```
Tool:    bedtools closest (aka closestBed)
Version: v2.23.0
Summary: For each feature in A, finds the closest
         feature (upstream or downstream) in B.
...
    -d    In addition to the closest feature in B, 
          report its distance to A as an extra column.
          - The reported distance for overlapping features will be 0.
```