Hello Chris,

Thank you for reporting the problem, it was indeed a calculation error with the BED-to-Codon operation. The code has been corrected, but has not been placed onto the Galaxy main server yet. Look for it in the next week and please let us know if you have more comments.


Thanks again!

Best,

Jen
Galaxy team

On 3/22/11 4:52 AM, Christopher Schroeder wrote:
Hello list,

I already analysed some of our data with your framework and I want to
thank you for your great work. But lately I stumbled on some strange
behavior - I used the “aaChanges”-tool, as well as the Gene
“BED-to-Codon”-tool with the same Gene-BED-File and compared the
results. What I did:

#example BED-file:

chr17      3763624 3794037 uc002fwt.2          0              -              
3765504 3788981 0              16                
1953,104,129,88,74,54,200,89,22,37,134,52,54,48,403,51,                
0,5577,9156,9470,12223,13078,15892,20015,21296,22197,22711,23098,23553,24049,24997,30362,

#example-output of “aaChanges”

chr17 3775847 3775848 C uc002fwt.2 Glu:Gly 375 T

#example-output of “BED-to-Codon”

chr17      3773172 3773175 uc002fwt.2          0              -

chr17      3773175 3773178 uc002fwt.2          0              -

chr17      3773178 3773181 uc002fwt.2          0              -

chr17      3775849 3775852 uc002fwt.2          0              -

chr17      3775852 3775855 uc002fwt.2          0              -

Comparing both results, the “BED-to-Codon” actually presents no codon at
position 3775848 – here the fist codon is starting at 3775849. But in
fact, looking at the ucsc browser, “aaChanges” is right. There are
another few examples (~5/1500 snps) and apparently most of them are
positions among the first codon in an exon.

Did anyone meet this problem before? What is my mistake?

Thank you.

Regards

Chris



___________________________________________________________
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
___________________________________________________________
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/

Reply via email to