Ns126:Calendar/NOTES/2015-10-16

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Missing value in MHL matrix

  • 1, 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.
  • 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

/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/mld_blocks_July2015WGBS_SeqCap_methHap_load_matrix_16Oct2015.txt