Ns126:Calendar/NOTES/2015-10-16: Difference between revisions

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==Missing value in MHL matrix==
==Missing value in MHL matrix==


*1, in the line 169 of /home/k4zhang/bin/mergedBam2hapInfo_WGBS_25Jun15.pl  in TSCC
* in the line 169 of /home/k4zhang/bin/mergedBam2hapInfo_WGBS_25Jun15.pl  in TSCC
*the methylation haplotype were not output. therefore, even we remove the mentioned constraint, the methylation haplotype would be longer than 3.   
*the methylation haplotype were not output. therefore, even we remove the mentioned constraint, the methylation haplotype would be longer than 3.   
* in the line 169 of /home/shg047/monod/haplo  next if(scalar(@valid_positions)<3) were replaced with  next if(scalar(@valid_positions)<1);
* here, <1 is to filter out output whose haplotstring is ""(NULL)
* in the line 170 of /home/shg047/monod/haplo next if($valid_hap =~ /AG/) were replaced with next if($valid_hap =~ /[AG]/)
             


*2, In the line 26 and 27 of /home/k4zhang/bin/mergedBam2hapInfo_WGBS_25Jun15.pl
*2, In the line 26 and 27 of /home/k4zhang/bin/mergedBam2hapInfo_WGBS_25Jun15.pl

Latest revision as of 17:35, 20 October 2015

Missing value in MHL matrix[edit]

  • in the line 169 of /home/k4zhang/bin/mergedBam2hapInfo_WGBS_25Jun15.pl in TSCC
  • the methylation haplotype were not output. therefore, even we remove the mentioned constraint, the methylation haplotype would be longer than 3.
  • in the line 169 of /home/shg047/monod/haplo next if(scalar(@valid_positions)<3) were replaced with next if(scalar(@valid_positions)<1);
  • here, <1 is to filter out output whose haplotstring is ""(NULL)
  • in the line 170 of /home/shg047/monod/haplo next if($valid_hap =~ /AG/) were replaced with next if($valid_hap =~ /[AG]/)


  • 2, In the line 26 and 27 of /home/k4zhang/bin/mergedBam2hapInfo_WGBS_25Jun15.pl
my @unmethylated_haps= ("T", "TT", "TTT", "TTTT", "TTTTT");
my @methylated_haps= ("C", "CC", "CCC", "CCCC", "CCCCC");
my @unmethylated_haps= ("T", "TT", "TTT", "TTTT", "TTTTT","TTTTTT","TTTTTTT");
my @methylated_haps= ("C", "CC", "CCC", "CCCC", "CCCCC","CCCCCC","CCCCCCC");


it means the haplotype whose length is longer than 5 would be ignore.

  • Therefore, actually, we only consider the haplotype whose length is 4 and 5.

Updated methylation haplotype load for WGBS, RRBS and SeqCap Dataset[edit]

/home/kunzhang/CpgMIP/MONOD/Data/WGBS_data/mld_block_hapInfo_July2015/All_chromosomes_combined
/home/kunzhang/CpgMIP/MONOD/Data/1407-combined_RRBS/mld_blocks_hapInfo_July2015
/home/kunzhang/CpgMIP/MONOD/Data/150209_SN216/SeqCap/mld_blocks_July2015
/home/kunzhang/CpgMIP/MONOD/Data/WGBS_data/mld_block_hapInfo_July2015/All_chromosomes_combined/WGBS_methHap_load_matrix_16Oct2015.txt
/home/kunzhang/CpgMIP/MONOD/Data/1407-combined_RRBS/mld_blocks_hapInfo_July2015/RRBS_methHap_load_matrix_16Oct2015.txt
/home/kunzhang/CpgMIP/MONOD/Data/150209_SN216/SeqCap/mld_blocks_July2015/WGBS_SeqCap_methHap_load_matrix_16Oct2015.txt