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--- project:opensnp [2015/06/06 18:23] – [Doing a PCA w/ openSNP data] gedankenstuecke
+++ project:opensnp [2015/06/06 18:29] – [Doing a PCA w/ openSNP data] gedankenstuecke
@@ Line 7: / Line 7: @@
 ==== Doing a PCA w/ openSNP data ====
+[[https://dl.dropboxusercontent.com/u/170329/pca-opensnp.png|{{https://dl.dropboxusercontent.com/u/170329/pca-opensnp.png?350}}]]
 This is done in multiple steps with the help of PLINK and SmartPCA:
@@ Line 66: / Line 68: @@
   * The plots here were done on all SNPs, not the subsampled ones (as I didn't notice that it wasn't done automatically…). Should re-run it on the less autocorrelated set
   * Right now the scripts for generating all the data are messy at best and can't be run automatically, should be fixed
+  * Include the 1000Genomes data, not done so far.
   * Go wild!
 ===== Data =====
@@ Line 79: / Line 82: @@
   * Repo for doing PCA on openSNP: https://github.com/ciyer/opensnp-fun
+  * [[https://github.com/gedankenstuecke/opensnp-fun|@gedankenstuecke's fork of ciyer's repo]]
-{{tag>status:concept needs:dev needs:design needs:data needs:expert}}
+  * [[http://www.nature.com/nature/journal/v456/n7218/fig_tab/nature07331_F1.html|The figure we tried to reproduce]]
+  * [[https://www.cog-genomics.org/plink2/strat|PLINK manual]]
+{{tag>status:demo needs:dev needs:design needs:data needs:expert}}