Question: Snp Annotation
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gravatar for Oliver, Gavin
7.0 years ago by
Oliver, Gavin20 wrote:
Hi, I am new to Galaxy and am wondering what tools are available for annotation of SNPs? I know that snpEff is implemented in Galaxy and this enables annotation such as location and predicted effect, however I am wondering if there are any automated means of annotating a polymorphism as known/novel or determining its frequency in the population. Does Galaxy offer anything like this or would it be necessary to create scripts that would for exampole compare to dbSNP for uniqueness and the 1000 genomes project for frequency. Best, Gavin The contents of this message and any attachments to it are confidential and may be legally privileged. If you have received this message in error, you should delete it from your system immediately and advise the sender. Almac Group (UK) Limited, registered no. NI061368. Almac Sciences Limited, registered no. NI041550. Almac Discovery Limited, registered no. NI046249. Almac Pharma Services Limited, registered no. NI045055. Almac Clinical Services Limited, registered no. NI041905. Almac Clinical Technologies Limited, registered no. NI061202. Almac Diagnostics Limited, registered no. NI043067. All preceding companies are registered in Northern Ireland with a registered office address of Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK. Almac Sciences (Scotland) Limited, registered in Scotland no. SC154034. Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are Delaware limited liability companies and Almac Group Incorporated is a Delaware Corporation. More information on the Almac Group can be found on the Almac website: www.almacgroup.com
snpeff snp • 837 views
ADD COMMENTlink modified 7.0 years ago by Jennifer Hillman Jackson25k • written 7.0 years ago by Oliver, Gavin20
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gravatar for Jennifer Hillman Jackson
7.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello Oliver, You can compare SNP datasets using the tools under "RGENETICS" and "Human Genome Variation". dbSNP and 1000 Genomes data are locally cashed in our Libraries, making them easy to load into a history and use. Also, here is an example workflow that includes sample SNP analysis (dbSNP vs 1000 genomes): http://main.g2.bx.psu.edu/u/ericy/p/chry-1000-genomes Hopefully this helps, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
ADD COMMENTlink written 7.0 years ago by Jennifer Hillman Jackson25k
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