Hello Richard,
The coordinates have a zero-based start. Add +1 to the start, do nothing to the end, and the bases included will match up with any visualization tool where the first base is labeled "1".
The data: chr10 1056309 1056310 G C +
start = 1056309 + 1 = 1056310 end = 1056310 SNP is a single base change at position = 1056310
There are other details, but this is the key fact that you will likely need to know for most applications, esp. those that are not stranded or converted to be on the (+) strand.
For the full details, including how to transform (-) stranded coordinates using this system, the description from UCSC is very handy: http://genomewiki.cse.ucsc.edu/index.php/Coordinate_Transforms
Hopefully this helps,
Best,
Jen Galaxy team
On 9/11/11 8:04 PM, Richard Mark White wrote:
Hi, This must seem like a newbie question but I cant get a clear answer. My understanding from the galaxy wiki page http://wiki.g2.bx.psu.edu/Learn/FAQ#Learn.2BAC8-FAQ.Interval_and_BED_format is 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!
rich
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