Noi/NOTES/2012-3-19
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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)
- Filter out CpG-SNP methylMatrix using remove_snps.pl: Media:remove_snps.txt written by Dr. Zhang
../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%
- Two examples of heritables CpG sites: by running extract_trios_methyl_values.pl: File:Extract trios methyl values.txt written by Dr. Zhang
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
- Note:
- Red = no SNP CPG
- Blue = SNP-CpG
- Gray scale represent gene density
- Continued on: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-19