[BioC] export funciton alters ranges in output BED file

[John Blischak]

Hi Dolev,

On Sun, Sep 14, 2014 at 9:42 AM, do r <dolevrahat at gmail.com> wrote:
> However, the ranges in the output file are altered so that the start
> coordinate is subtracted by one,
>
> Since I intend to later to searrch for intersections between the
> ranges in the BED file and variants in a vcf file (using Tabix), I am
> afraid that this subtratcion may lead to false positive.
>
> What is the reason for this subtraction from the start and is there
> any way to supress it?

You do not want to supress this behavior. This is how BED files are
formatted. The coordinates are 0-based, with the start site being
inclusive and the end site being exclusive. This is the format that
BEDTools will expect when you are performing your intersections. Here
are some links to learn more:

http://www.genome.ucsc.edu/FAQ/FAQformat.html#format1
http://genome.ucsc.edu/FAQ/FAQtracks#tracks1
https://www.biostars.org/p/89341/#89406
https://www.biostars.org/p/84686/

Best,

John