Dinh 2011/NOTES/2011-11-17
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MUIR samples from Yang Xu's lab[edit]
- 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[edit]
- 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[edit]
# 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[edit]
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[edit]
- 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.