Hello Maha,
This does sound very strange. Would you please share a link to your
history so that we can examine the data and determine where the problem
originates? Please note which dataset contains this particular problem
if there are several runs from this same tool.
Use "Options -> Share of Publish", generate the share link with the top
button, copy the URL, and paste it into a reply email sent back to me
directly.
Thank you!
Jen
Galaxy team
On 3/9/12 8:28 AM, Maha Al Kahtani wrote:
Hello,
Recently i have used galaxy to find corresponding amino acids to a list
of SNPs that i have. i used aaChange tool from the tool panel for this
purpose. After obtaining the result i checked the correctness of this
results by searching dbSNP for randomly chosen SNPs. however, some of
those SNPs mapped to incorrect amino acid,
For example,
The SNP( rs11549096), was mapped by Galaxy to the change ( Asp:Tyr/His,
) , Searching the dbSNP for this SNP Shows that the Change should be
Asp :Asn and the link for this SNP in the dbSNP is :
http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?searchType=adhoc_search&type=rs&rs=rs11549096
<http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?searchType=adhoc_search&type=rs&rs=rs11549096>
So, the reference is correct in all cases i searched (more than a
thousand), the position of change in the aa is correct, _*but*_ the
alternative aa is not correct in all cases.
What causes this mistake, and how to solve this problem?
Note: my list contains hundreds of thousands of SNPs, so, i can not
check each one of them.
prompt response is appreciated,
Best Regards,
Maha
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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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
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