Question: Help with SNP to Gene mapping
2
gravatar for ptdikshi
2.5 years ago by
ptdikshi20
ptdikshi20 wrote:

Hi, I am new to the domain of bioinformatics and am looking to use computational methods on some WGS (Whole genome sequencing) SNP data. I have a list of 1276349 SNPs which I wish to map to corresponding genes. I have tried using BioMart - but its server is unavailable, due to which am not able to use this resource. I have heard that the 'Galaxy' browser can be used to perform such mappings for large sized data. I would appreciate any pointers on how I can get this done quickly! . Thanks in advance!

snp galaxy • 921 views
ADD COMMENTlink written 2.5 years ago by ptdikshi20
2
gravatar for Guy Reeves
2.5 years ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

have you looked at NGS: Variant Analysis>SnpEff Variant effect and annotation.

there is nice help for this tool http://snpeff.sourceforge.net Though note that there may be differences at the version on usegalaxy.org might not always be the most up to date one

If you are using mouse or human then the database is already loaded on usegalaxy.org. if not there are tools in the NGS: Variant Analysis section to download them. Cheers Guy

ADD COMMENTlink written 2.5 years ago by Guy Reeves1.0k
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