fixed number of bins with makewindows

[Aarthi Mohan]

Hi,

This might be a very trivial doubt, but I would like to know how makewindows partition a given interval when we use -n (fixed number of windows). 

Example of what I see in my case:

bedtools makewindows -b test1.bed -n 10 -i srcwinnum

chr1    11      15      xxxxx_1

chr1    15      19      xxxxx_2

chr1    19      23      xxxxx_3

chr1    23      27      xxxxx_4

chr1    27      31      xxxxx_5

chr1    31      35      xxxxx_6

chr1    35      39      xxxxx_7

chr1    39      43      xxxxx_8

chr1    43      44      xxxxx_9

Why is it am getting 9 bins instead of 10? Same thing happens for the some genes in my annotation file, where I get less than 'n' bins. 

Bedtools version: 2.25.0

Thanks for your help!

Best,

Aarthi

[Aaron Quinlan]

Thanks for reporting this, Aarthi. It looks like an accounting bug and I will look into resolving it.

Best,

Aaron

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[Gokhul Krishna Kilaru]

Thanks Aaron. Even I was having the same issue.

[Aarthi Mohan]

Thanks Aaron, it will be really helpful.

Regards,

Aarthi

[Aaron Quinlan]

Hi Aarthi,

Thanks again for reporting this - I have addressed it and the fix is in the repository on github (https://github.com/arq5x/bedtools2)

$ bedtools makewindows -b test1.bed -n 10 -i srcwinnum

1 11 14 A_1

1 14 17 A_2

1 17 20 A_3

1 20 23 A_4

1 23 26 A_5

1 26 29 A_6

1 29 32 A_7

1 32 35 A_8

1 35 38 A_9

1 38 44 A_10

I have also added a warning when an interval’s length is less than the number of bins requested:

$ cat test2.bed

1 10 19 B

bedtools makewindows -b test2.bed -n 10 -i srcwinnum

WARNING: Interval 1:10-19 is smaller than the number of windows requested. Skipping.