Makewindows doesn't create the correct number of windows

[niran...@gmail.com]

I am running the following command

bedtools makewindows -b Input.bed -n 100 -i src > Out.bed

Where the input file has variable sizes of genomic regions of interest. I removed all the regions that were below 200bp (largest regions is 100,000bp) and run the command. No error was received but it didn't create the correct amount of windows to all of the regions. Most regions did have 100 windows but the rest did not. I was wondering if this is known problem and if there are any limitation on running makewindows as far as region length/window size ratio. i.e I have a 1000bp region, I can only make <100 windows.

Thanks,

Niran

[Aaron Quinlan]

Hi Niran,

While it is not mentioned on the release notes (apologies), there was a bug related to this that was fixed prior to the 2.26.0 release. Could you retry with the latest version on github (https://github.com/arq5x/bedtools2). If you still have trouble, could you provide a minimal example?

Thanks,

Aaron

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[Niran Hadad]

I wrote an alternative but I'll give it a go anyway and let you know. 

Thanks for the help,

Niran

[Niran Hadad]

Just wanted to update. run bedtools makewindow with bedtools 2.26 and it worked fine.

Thank you,

Niran

On Thursday, September 15, 2016 at 10:24:34 AM UTC-5, Aaron Quinlan wrote: