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... 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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