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=== methyhaplotype to matrix=== * transfer haplotype result (per chrosome per sample) to genome miner * methylation haplotype load (mhl) matrix cp /home/kunzhang/CpgMIP/MONOD/Data/WGBS_data/mld_block_hapInfo_July2015/All_chromosomes_combined/WGBS_methHap_load_matrix_Oct2015.txt /home/shg047/monod/oct/data/ cp /home/kunzhang/CpgMIP/MONOD/Data/1407-combined_RRBS/mld_blocks_hapInfo_July2015/RRBS_methHap_load_matrix_Oct2015.txt /home/shg047/monod/oct/data/ cp /home/kunzhang/CpgMIP/MONOD/Data/150209_SN216/SeqCap/mld_blocks_July2015/WGBS_SeqCap_methHap_load_matrix_Oct2015.txt /home/shg047/monod/oct/data/ * [[tissue specific mhl regions]] * extract raw methylation signals within above regions(multiple cpg site in each regions) ** [[extract CpG site within above regions]] * extract absolute methylation levels within above regions(one value in each regions) * Bam files: ESC, Ecker, N37, age, Plasma were in the TSCC center /home/k4zhang/my_oasis_tscc/MONOD/hESC_WGBS/BAMfiles/ /home/k4zhang/my_oasis_tscc/MONOD/Ecker_Tissue_WGBS/BAMfiles /home/k4zhang/my_oasis_tscc/MONOD/N37_WGBS/BAMfiles /home/k4zhang/my_oasis_tscc/MONOD/whole_blood_WGBS/BAMfiles/ /home/k4zhang/my_oasis_tscc/MONOD/tumor_WGBS/BAMfiles/ * # chr17:16955467-16955609 in Colon_primary_tumor.chr17.sorted.clipped.bam samtools tview -p chr17:16955467 /home/k4zhang/my_oasis_tscc/MONOD/tumor_WGBS/BAMfiles/Colon_primary_tumor.chr17.sorted.clipped.bam /home/shg047/db/hg19.fa * # chr11:110910907-110910951 in middle-age.chr11.rmdup.bam samtools tview -p chr11:110910907 /home/k4zhang/my_oasis_tscc/MONOD/whole_blood_WGBS/BAMfiles/middle-age.chr11.rmdup.bam /home/shg047/db/hg19.fa * # grep chr11:110910907-110910951 in hapInfo files of middle-age.chr11.hapInfo.txt grep chr11:110910907-110910951 /home/kunzhang/CpgMIP/MONOD/Data/WGBS_data/mld_block_hapInfo_July2015/by_chrosomes/middle-age.chr11.hapInfo.txt grep chr11:110910907-110910951 /home/shg047/monod/hap/wgbs/All_chromosomes_combined/WB_middle-age.all_chrs.hapInfo.txt
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