Dinh 2011/NOTES/2011-11-5

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Revision as of 02:33, 9 November 2011 by >Dinh
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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
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]

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