That is consistent with the BED format, that is in "BEDs" 0 based coordinate
system the SNP is at 1056309. In the more common "1" based system this
translates to 1056310. If the end were inclusive the SNP would be at
1056309-1056310 in "BED" world, that is it would take 2 positions.
The first base of a genome in BED coordinates is represented as 0-1.
My quick rule of thumb for converting between coordinate systems is to add
(or subtract) 1 from the start base, leave the end base alone.
On Sun, Sep 11, 2011 at 10:58 PM, Richard Mark White <whit...@yahoo.com>wrote:
> This must seem like a newbie question but I cant get a clear answer. My
> understanding from the galaxy wiki page
> that all intervals in galaxy are 0 based, start inclusive end exclusive.
> but when i use generate pileup/filter pileup and convert to intervals, i
> get something like this:
> chr10 1056309 1056310 G C +
> When i look up the SNP (G-->C) it is pretty clearly 1056310. Which would
> make the "interval" end inclusive. this is key because when i annotate
> snp's against dbSNP, i need to have the right cooridnates.
> Can anyone provide some guidance? Thanks!
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The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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