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==MUIR samples from Yang Xu's lab== * 2HFF_P6 is progenitor for 2HFF8d_10 * 218HFF_P7 is progenitor for 218HFF411 and 218HFF211 ** Note that: '''218HHF*''' is how the files are originally file names, I changed the HHF to HFF for the end analysis * Number of CpG captured in each sample (no CG-SNP): 418477 218HFF_P7.txt.cg-pos.BED.txt 375514 218HFF211.cg-pos.BED.txt 351674 218HFF411.cg-pos.BED.txt 432937 2HFF8d_10.cg-pos.BED.txt 504668 2HFF_P6.txt.cg-pos.BED.txt 404638 Hues1.txt.cg-pos.BED.txt 309784 Hues3.txt.cg-pos.BED.txt 458459 Hues8.txt.cg-pos.BED.txt * Number of CG-SNP in each sample: 13035 218HFF_P7.txt.cSNP-pos.BED.txt 11524 218HFF211.cSNP-pos.BED.txt 10799 218HFF411.cSNP-pos.BED.txt 13146 2HFF8d_10.cSNP-pos.BED.txt 15490 2HFF_P6.txt.cSNP-pos.BED.txt 12433 Hues1.txt.cSNP-pos.BED.txt 9614 Hues3.txt.cSNP-pos.BED.txt 14041 Hues8.txt.cSNP-pos.BED.txt ===Memory/Mutation=== *First to use '''getCpG*11082011.pl''', need a set of allowable sites! awk '{print $1"\t"$3;}' Hues*.BED.txt | sort -u > H1H3H8_allsites wc -l H1H3H8_allsites '''502459''' *Compare Hues1vsHues3, Hues1vsHues8, Hues3vsHues8: Test, #comparable sites, #different sites 1vs3 233,817 2130/233817 = 0.9% 1vs8 307,055 3619/307055 = 1.2% 3vs8 243,655 1657/243655 = 0.7 *Find variable sites: less *dmTable | awk '{if($2==1) print $0;}' | sed 's/:/\t/g' | awk '{print $1"\t"$2}' | sort -u > variableH1H3H8 wc -l variableH1H3H8 '''4862''' *Reform subset sites list: cat variableH1H3H8 variableH1H3H8 H1H3H8_allsites | sort | uniq -u > H1H3H8_filteredsites wc -l H1H3H8_filteredsites '''497597''' *Run GO.calcMEMMU.sh #Set up mf tables such that first test compare to ES and second test compare to SOM for f in mf_*.txt do ./getCpgChsq+DiffMatrix_DD_*.pl $f 10 0.2 0.001 H1H3H8_filteredsites > $f.dmTable awk ' function abs(value) { return (value<0?-value:value) }; { if($2==1 && $3==1 && abs($4-$5) >= 0.2 && ( ($4<0 && $5>=0) || ($4>0 && $5<=0) )) print $0,"\tMEMORY_INCOMPLETE"; if($2==1 && $3==0 && abs($4-$5) >= 0.2 && abs($5) < 0.2 && abs($4) > abs($5) ) print $0, "\tMEMORY_COMPLETE"; if($2==1 && $3==1 && ( ($4<0 && $5<0) || ($4>0 && $5>0) )) print $0, "\tMUTATION"; if($2==0 && $3==1 && abs($4)<0.2) print $0,"\tPLURIPOTENCY"; } ' $f.dmTable > $f.memmuTable done; ===Results=== # total sites tested 212239 mf_218HFF211.txt.dmTable (1350 memory, 530 mutations) 193521 mf_218HFF411.txt.dmTable (2162 memory, 586 mutations) 244023 mf_2HFF8d_10.txt.dmTable (2144 memory, 1101 mutations) ===Genome browser shots=== Each loci was picked randomly from a list of memory or mutation sites. [[File:Muir-MemoryMutation-TCERG1L.png]] [[File:Muir-MemoryMutation-IRS2.png]] [[File:Muir-MemoryMutation-HOX.png]] ===Scatter plots=== *Distances are iPS - ES or iPS - SOM *It looks like more memory sites are due to difficulty getting '''methylated''' - iPS is less methylated than ES. *And more mutation sites are due to sites getting '''methylated''' when it should not be. [[File:Muir-MemoryMutation-scatterplot.png]]
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