Noi/NOTES/2013-3-26

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Revision as of 19:51, 26 March 2013 by >Noi (Created page with "== mQTL analysis on 5M SNPs (UCLA data set) == * Actually I finished analysis on these SNPs already, but there were some job exceed the limited walltime and got killed. I repe...")
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mQTL analysis on 5M SNPs (UCLA data set)

  • Actually I finished analysis on these SNPs already, but there were some job exceed the limited walltime and got killed. I repeat analysis again by splitting methylFreq to be smaller (3000 CpGs/job)
  • Working directory on Triton cluster: /oasis/triton/scratch/nplongthongkum/20130219_UCLA_SZ_mQTL/20130324_mQTL_5M.SNPs_maf0.1_repeat
  • Data summary
    • Total tested CpGs: 76,408 autosomal CpGs
    • Total tested SNPs: 5,257,772 SNPs
    • Total number of tests: 445,603,530
- Copy all output onto genome-miner: /home/nplongth/Noi_scratch/DataAnalysis_2013/UCLA_mQTL_5MSNPs_repeat_20130326
- Printout all output and sort out p-value
cat mQTL-maf0.1.xa* | awk '{if($1~/chr/) print $0}' |sort -g -k7 -k6 > all.mQTL-maf0.1.output