Dinh 2011/NOTES/2011-9-29: Difference between revisions

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  2182  head -70000 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -10000 > no_60001_70000/UPenn46_hg19_methylMatrix_filtered_60001-70000.txt
  2182  head -70000 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -10000 > no_60001_70000/UPenn46_hg19_methylMatrix_filtered_60001-70000.txt
  2183  tail -7573 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt > no_70001_77573/UPenn46_hg19_methylMatrix_filtered_70001-77573.txt
  2183  tail -7573 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt > no_70001_77573/UPenn46_hg19_methylMatrix_filtered_70001-77573.txt
'''I found out that the PennAfrican_Batch1_genotypes file has SNP positions in build 36.3 and not in build 37.1'''
'''Wrote script to lift over snp's RS values to hg19 positions'''
[[File:liftOverRSvalues.txt]]

Revision as of 01:02, 4 October 2011

Penn African mQTL

./mQTL_2MB_plink.pl ../PennAfrican_Batch1_genotypes ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt > results.txt &

Divided high variance methylation matrix (77563 CpGs) to 8 groups:

2176  head -30000 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -10000 > no_20001_30000/UPenn46_hg19_methylMatrix_filtered_20001-30000.txt
2179  head -40000 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -10000 > no_30001_40000/UPenn46_hg19_methylMatrix_filtered_30001-40000.txt
2180  head -50000 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -10000 > no_40001_50000/UPenn46_hg19_methylMatrix_filtered_40001-50000.txt
2181  head -60000 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -10000 > no_50001_60000/UPenn46_hg19_methylMatrix_filtered_50001-60000.txt
2182  head -70000 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -10000 > no_60001_70000/UPenn46_hg19_methylMatrix_filtered_60001-70000.txt
2183  tail -7573 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt > no_70001_77573/UPenn46_hg19_methylMatrix_filtered_70001-77573.txt

I found out that the PennAfrican_Batch1_genotypes file has SNP positions in build 36.3 and not in build 37.1 Wrote script to lift over snp's RS values to hg19 positions

File:LiftOverRSvalues.txt