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Old 07-24-2012, 05:50 AM   #1
Cantabulous
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Location: Cambridge

Join Date: Jul 2012
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Default Best way to get 1.3m genome positions for rsIDS (EMMAX output)?

Hello, it's my first post so please be gentle!

I have EMMAX GWAS output - RSid beta p-value. I need to get the chromosome number and position for these data so that I can make Manhattan plots. Can anyone suggest the best way to do this? I've never used the Ensembl perl API, but I've seen some references to Bioconductor packages? I use R but not Bioconductor.

I do have a Python script that matches up lines, so I could run it against some PLINk output that incls chrN, pos and RSids - but it took 2 days to run matching 500k SNPs, so 1.3m will be a LOT worse!
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