hi, I would like to create a list of random mm10 genomic coordinates with bedtools. I saw that the useful command to do this is `bedtools random [OPTIONS] -g <GENOME>`. The problem is that they must have different length, similar to my coordinates:

    > summary (new $ width)
       Min.  1st Qu.   Median   Mean   3rd Qu.   Max.
        188    1645     2649   2904    4196      11484

is there any other tool that can set different lengths when generating coordinates?
Thank you!


There are a couple of different ways to approach this, I think, depending on what you have on hand. If you already have a set of coordinates such as the ones you've entered above, you could simply shuffle these coordinates along the genome using bedtools [shuffle][1]. If you only have a small list of such regions and need a relatively large amount, you could perform the operation repeatedly to get a large number of such regions.

Alternatively it looks like there is an R package for this task. I've not used it myself, but the documentation is [here][2].


  [1]: https://bedtools.readthedocs.io/en/latest/content/tools/shuffle.html
  [2]: https://rdrr.io/bioc/regioneR/man/createRandomRegions.html