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:
http://lists.bx.psu.edu/
___________________________________________________________
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:
http://lists.bx.psu.edu/