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
___
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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
___
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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
