Question: bedtools - shuffle with overlapping even if -noOverlapping option activated
gravatar for m.o.baudement
20 months ago by
m.o.baudement10 wrote:

Hi everybody, After different tries, I realize one thing about the BEDtools tool ShuffleBED and I will be happy to have some feedback about it and know if this problem was already seen by someone else. What I would like to do is easy : randomize the genomic regions I have, to see if the criteria of these regions are unexpected or not. On shuffleBED, I use options where I respect the distribution of my regions by chromosome, I exclude unmappable regions, and I exclude the possibility to have overlaps.

After analysis of the random file I obtained, the chromosome location are respected, the size of my genomic regions too, but I see that some genomic regions overlap between them. This effect is less important (divided by around 4) if I multiply by 10 the number of Tries for the positioning (maxTries option). But at the end, they are still some domains that overlap. I suppose that it's depends of how many regions, and furthermore, what are the size of the regions that are already re - place by random. Indeed, if lot of short regions are already positionned, there is less and less possibility to have large space to place a large region. So shuffleBED return the last found position by random to put the big region, even if this position overlap with another region. Am I right on my understanding of the work of this tool ? Finally, my question is the following : is someone else has already observed this problem, how to manage with ?

I thought to order my input file thanks to length of the regions that I want to randomly positioned, But first of all, this bias the randomization, and secondly, ShuffleBED randomize the size of the regions to position. So it's not the solution. So what else ?

Thank you for your feed back.

I will appreciate your help.

  • MO -
ADD COMMENTlink modified 20 months ago • written 20 months ago by m.o.baudement10
gravatar for Jennifer Hillman Jackson
20 months ago by
United States
Jennifer Hillman Jackson25k wrote:


If you think you found a bug with this BEDTools function, reporting it to the tool authors is how to find out if it is a known and if there are plans to correct it. This is the google discussion group for the tool, and there are some posts about this tool, but I didn't see a reported problem:!forum/bedtools-discuss

If you would like to vet the problem first to make certain there is a not a tool wrapper problem (none are known right now), follow the instructions for sharing a history link and we can review (I am assuming that the job is not a failure, just that the results are unexpected):

Thanks, Jen, Galaxy team

ADD COMMENTlink written 20 months ago by Jennifer Hillman Jackson25k
gravatar for m.o.baudement
20 months ago by
m.o.baudement10 wrote:

OK thank you. I will do it tomorrow.

ADD COMMENTlink written 20 months ago by m.o.baudement10
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