Dinh 2011/NOTES/2011-11-5
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Memory / Mutation calling[edit]
- create a list of previously called sites (from first samples set) for sites subsetting:
awk '{print $1,"\t", $2}' *.methylFreq | sed 's/ //g' | sort -u > subsetted_sites_11052011 wc -l subsetted_sites_11052011 1359254
- find all sites covered at 10x in both H1 and H9:
less H1.methylFreq.BED.txt.gz H9.methylFreq.BED.txt.gz | awk '{print $1,"\t",$3;}' | sed 's/ //g' | sort | uniq -d > /home/dinh/H1_H9_rd10_sites_11082011
- filter .methylFreq files for H1 and H9:
less ../MethylFreq_Files/LibraryFree_methylFreq/trimmed.H1andH9combo.methylFreq | ./getDataAtSites.pl ../H1_H9_rd10_sites_11052011 > H1andH9combined_bothRD10.methylFreq_11082011
- create mf_PGP1iPS1.txt file: NOTE: I am trying to see if I can get the same results that Athurva did previously.
hESC H1andH9combined_bothRD10.methylFreq_11082011 PGP1F ../MethylFreq_Files/LibraryFree_methylFreq/trimmed.PGP1F.fastq.fwd.pileup.methylFreq PGP1iPS-1 ../MethylFreq_Files/LibraryFree_methylFreq/trimmed.PGP1iPS-1.fastq.fwd.pileup.methylFreq TEST: vsES 2:0 TEST: vsSOM 2:1
- Run GO.calcMEMMU.sh (script below, depends on File:GetCpgChsq+DiffMatrix DD 11052011.txt)
for f in mf_PGP1iPS1.txt do ./getCpgChsq+DiffMatrix_DD_11052011.pl $f 10 0.2 0.001 subsetted_sites_11052011 > $f.dmTable awk ' function abs(value) { return (value<0?-value:value) }; { if($2==1 && $3==1 && ( ($4<0 && $5>=0) || ($4>0 && $5<=0) )) print $0,"\tMEMORY_INCOMPLETE"; if($2==1 && $3==0 && 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;
- 11-08-2011 edit
for f in mf_PGP1iPS1.txt do ./getCpgChsq+DiffMatrix_DD_11052011.pl $f 10 0.2 0.001 subsetted_sites_11052011 > $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]
- File:Mf PGP1iPS1.txt.memmu.txt
- File:Mf PGP1iPS1.txt.dm.txt 212,936 sites
2407 mutation sites 5916 memory sites * 11-08-2011 The numbers are lower now because I filtered out sites which: did not fulfill the fct >= 0.9 requirement did not have at least 10x CT coverage in both H1 and H9 for memory require a distance of >=0.2 for ES and SOM