error in bedtools merge

[Y Z]

Hi,

I hope this post is not a duplicate post. My last post seems to be gone...

So I have a bed file containing the following two lines:

NC_000962.3     1169440 1169440 92_region_15
NC_000962.3     1169440 1169445 84_region_2

I used 'bedtools merge' to merge these two lines but I got:

NC_000962.3     1169439 1169445

The start is minus one of the original start point. I don't know if I shouldn't allow point in a bed file (as the first line) or this is a bug?

[Aaron Quinlan]

In BED format, start is zero-based, so a single nucleotide would have start 1 less than end. Furthermore, in a zero-based, half-open coordinate system, start==end indicates an insertion between nucleotides.

 

https://www.biostars.org/p/84686/

 

Therefore, the flanking nucleotides are affected. Thus, merge updates the start to reflect that the merger of the two intervals includes that flanking nucleotide.

 

Aaron

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