Dinh 2011/NOTES/2011-11-5: Difference between revisions

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>Dinh
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>Dinh
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Line 5: Line 5:
     ''' 1359254 '''  
     ''' 1359254 '''  
*find all sites covered at 10x in both H1 and H9:
*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_11052011
  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:
*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
  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.
*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
  hESC H1andH9combined_bothRD10.methylFreq_11082011
  PGP1F ../MethylFreq_Files/LibraryFree_methylFreq/trimmed.PGP1F.fastq.fwd.pileup.methylFreq
  PGP1F ../MethylFreq_Files/LibraryFree_methylFreq/trimmed.PGP1F.fastq.fwd.pileup.methylFreq
  PGP1iPS-1 ../MethylFreq_Files/LibraryFree_methylFreq/trimmed.PGP1iPS-1.fastq.fwd.pileup.methylFreq
  PGP1iPS-1 ../MethylFreq_Files/LibraryFree_methylFreq/trimmed.PGP1iPS-1.fastq.fwd.pileup.methylFreq
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*[[File:mf_PGP1iPS1.txt.memmu.txt]]  
*[[File:mf_PGP1iPS1.txt.memmu.txt]]  
*[[File:mf_PGP1iPS1.txt.dm.txt]]
*[[File:mf_PGP1iPS1.txt.dm.txt]]
  2411 mutations
  2407 mutations
  7112 memories
  7101 memories

Revision as of 23:53, 8 November 2011

Memory / Mutation calling

  • 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;

Results:

2407 mutations
7101 memories