Hello Maha,

Currently, the aaChanges tool accepts SNP input data in a format such as:

chr22  15660821  15660822  A/G
chr22  15825725  15825726  G/T
chr22  15827035  15827036  G

Where all of the SNP strings are reported with respect to the (+) strand. In your input dataset, the coordinates are with respect to the (+) strand, but the SNP string has data from both the (+) and (-) strand. If the SNP data from the (-) strand is reverse complimented, and then run through the tool, the correct amino acid changes result.

There are no tools in Galaxy to reverse compliment a SNP string, but perhaps you have access to a unix or other text editing resource that can help you to perform the transformation. Currently, this is the only usage option for the tool.

Our team has discussed the option of enhancing this tool to accept both (+) and (-) stranded SNP input. A ticket has been opened to track the progress of this request:
http://bitbucket.org/galaxy/galaxy-central/issue/735

Thank you,

Best,

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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