Noi/NOTES/2012-3-19

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Link to calendar: [[1]]

Mid-parent offspring (mpo) analysis[edit]

  • Note: This analysis had been done a couple month ago, but I just document it here.
  • Run script mpo_v2.pl Media:mpo_v2.txt written by Dr. Zhang

UCLA sample information:Media:UCLA_RO_96_sample_information_revised.txt

../mpo_v2.pl ../UCLA_OP_96_sample_information_revised.txt UCLA-4batches_methyl_min76_minSTD0.1 > UCLA-RO-mpo_out.txt
header of mpo_out --> chr_pos	valid_trios	pearson_r2	slope	t_test	heritable
  • Extract heritable sites
awk '{if($6 ~ /XX/) print $0;}' UCLA-RO-mpo_out.txt > UCLA-RO-mpo_out-heritable.txt 
# of heritable CpG sites = 14,815 = 18.6% (out of 79,604 sites)
../remove_snps.pl UCLA-4batches_methyl_min76_minSTD0.1 /media/nomeDB/HsGenome/snp134_snv.txt > UCLA-4batches_methyl_min76_minSTD0.1-noSNP
# of CpG without SNP = 61,665 sites
  • run mpo_v2.pl on the matrix with no SNP (added header to methylation matrix with no SNP)
../mpo_v2.pl ../UCLA_OP_96_sample_information_revised.txt UCLA-4batches_methyl_min76_minSTD0.1-noSNP > UCLA-RO-mpo_out-noSNP.txt 
# of heritable CpG sites  without SNP = 6,205 = 7.8% (out of 79,604 sites)
so the heritable sites → total 14,815 sites 
- with SNP = (14,815 - 6,205 ) = 8,609 sites  → 58% 
- without SNP =  6,205 sites  → % 42%

File:MPO-heritableCpG chr13-45146448.png File:MPO-heritableCpG chr14-88658493.png
Plotted all the heritable CpG sites along the chromosomes
File:HeritableCpG gene.densityBG.png