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 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
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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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
___________________________________________________________ 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:
participants (2)
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Jennifer Jackson -
Maha Al Kahtani