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==Missing value in MHL matrix== * 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== /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
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