Recently i have used galaxy to find corresponding amino acids to a
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
SNPs mapped to incorrect amino acid,
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
and the link for this SNP in the dbSNP is :
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
each one of them.
prompt response is appreciated,
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
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
button, copy the URL, and paste it into a reply email sent back to me
Currently, the aaChanges tool accepts SNP input data in a format such
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,
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
usage option for the tool.
Our team has discussed the option of enhancing this tool to accept
(+) and (-) stranded SNP input. A ticket has been opened to track the
progress of this request: