Question: Snp_Annotation
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gravatar for Lakatos, Anita
7.2 years ago by
Lakatos, Anita10 wrote:
Polymorphic variations were retrieved from a sequenced data (aligned to hg18). The output file contains the chr and the position but no (rs number). The tab delimited file with map extension is Chr pos # pos 1 82496 0 82496 1 91549 0 91549 1 98173 0 98173 1 696970 0 696970 Could you please let me know if there is way with galaxy to retrieve the rs number for these SNPs? I am open to any solution! Many thanks for your help, Anita Lakatos ________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
galaxy • 640 views
ADD COMMENTlink modified 7.2 years ago by Jennifer Hillman Jackson23k • written 7.2 years ago by Lakatos, Anita10
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gravatar for Jennifer Hillman Jackson
7.2 years ago by
United States
Jennifer Hillman Jackson23k wrote:
Hello Anita, It is possible to check your positions against a reference SNP database to see if there is overlap. This will link any known SNPs rs numbers. The recommended tools would be in "Operate on Genomic Intervals". Join would be a basic choice, but other Tools that merge/cluster the data may be of interest. To start, load your dataset and a dbSNP dataset. It would be quickest to load from "Shared Data -> Data Library" using the data in “Putative SNP phenotypes -> dbSNP130.txt". The dataset is sourced from hg18 dbSNP130. Please use the option "View information" (click on arrow next to data set name) to understand the contents and formatting. The idea would be to format your data also into Interval format, then Join. From a quick look at your sample, the chromosome names would have to be modified (add in "chr"), column 2 reduced in value by "1", and column 3 removed. Tools in "Text Manipulation" can help to do these tasks. Good luck with your project and please let us know if you need more help, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org
ADD COMMENTlink written 7.2 years ago by Jennifer Hillman Jackson23k
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