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====Repeat the analysis using a refined set of targets==== *The analyses above were performed based on a set of RRBS targets compiled based on the read depth of CpG sites in tumor data. Some of the target regions are fairly large, and contain many non-overlapping reads that cannot be directly compared in the haplotype analysis. *A different way to define the RRBS targets is based on the read depth distribution (not just CpG sites), which might better separate non-overlapping reads. *To test this idea, I compiled a new set of RRBS targets with the following steps. samtools merge /home/kunzhang/CpgMIP/Data/MONOD/1407-combined_RRBS/Primary_tumor_ALL.merged.bam 6-T-1_1.merged.bam 6-T-1_2.merged.bam 6-T-2_1.merged.bam 6-T-2_2.merged.bam 6-T-3_1.merged.bam 6-T-3_2.merged.bam 6-T-4_1.merged.bam 6-T-4_2.merged.bam 6-T-5_1.merged.bam 6-T-5_2.merged.bam 7-T-1_1.merged.bam 7-T-1_2.merged.bam 7-T-2_1.merged.bam 7-T-2_2.merged.bam 7-T-3_1.merged.bam 7-T-3_2.merged.bam 7-T-4_1.merged.bam 7-T-4_2.merged.bam 7-T-5_1.merged.bam 7-T-5_2.merged.bam PC-T-1_1.merged.bam PC-T-1_2.merged.bam PC-T-2_1.merged.bam PC-T-2_2.merged.bam PC-T-4_1.merged.bam PC-T-4_2.merged.bam PC-T-6_1.merged.bam PC-T-6_2.merged.bam PC-T-7_1.merged.bam PC-T-7_2.merged.bam samtools sort Primary_tumor_ALL.merged.bam Primary_tumor_ALL.sorted & nohup /home/kunzhang/softwares/bedtools-2.17.0/bin/bedtools genomecov -bg -split -ibam Primary_tumor_ALL.sorted.bam > Pimary_tumor_ALL.genomecov.bed & awk '$4>50 { print $1"\t"$2"\t"$3}' Primary_tumor_ALL.genomecov.bed | /home/kunzhang/softwares/bedtools-2.17.0/bin/bedtools merge -d 10 -i - > Primary_tumor_ALL.genomecov.RD50.merged.bed awk '$3-$2>80 {print $1"\t"$2"\t"$3"\t"$3-$2+1}' Primary_tumor_ALL.genomecov.RD50.merged.bed> Primary_tumor_ALL.genomecov.RD50_80UP.merged.bed sh [[media:1407-combined_expanded_31Aug14_step1_batch_command.txt|1407-combined_expanded_31Aug14_step1_batch_command.sh]] & ../../mixMethHapAnalysis_19Aug14.pl NC-P-ALL.hapInfo.txt 6-T-ALL.hapInfo.txt 6-P-ALL.hapInfo.txt /home/kunzhang/CpgMIP/MONOD/Public_data/WB_middle_age_UMR.BED.txt | sort -k 2,2nr > RRBS_targets_LOD_CC.txt & ../../mixMethHapAnalysis_19Aug14.pl NC-P-ALL.hapInfo.txt 7-T-ALL.hapInfo.txt 7-P-ALL.hapInfo.txt /home/kunzhang/CpgMIP/MONOD/Public_data/WB_middle_age_UMR.BED.txt | sort -k 2,2nr > RRBS_targets_LOD_LC.txt & ../../mixMethHapAnalysis_19Aug14.pl NC-P-ALL.hapInfo.txt PC-T-ALL.hapInfo.txt PC-P-ALL.hapInfo.txt /home/kunzhang/CpgMIP/MONOD/Public_data/WB_middle_age_UMR.BED.txt | sort -k 2,2nr > RRBS_targets_LOD_PC.txt & ./find_NC-P_high-LOD_targets.pl > NC-P_high-LOD_targets.txt ./filter_targets.pl RRBS_targets_LOD_PC.txt NC-P_high-PC-LOD_targets.txt | sort -k 2,2nr > RRBS_targets_LOD_PC_top_1914.txt ./filter_targets.pl RRBS_targets_LOD_LC.txt NC-P_high-LC-LOD_targets.txt | sort -k 2,2nr > RRBS_targets_LOD_LC_top_1629.txt ./filter_targets.pl RRBS_targets_LOD_LC.txt NC-P_high-CC-LOD_targets.txt | sort -k 2,2nr > RRBS_targets_LOD_CC_top_1487.txt ./get_all_CC-P_LOD.pl > CC-P_LOD_out.txt & ./get_all_LC-P_LOD.pl > LC-P_LOD_out.txt & ./get_all_PC-P_LOD.pl > PC-P_LOD_out.txt & *A total of 822 regions that contain cancer haplotypes in two or more samples were identified. [[Image:Colon_cancer_UMR_tumor_haplotype_load_31Aug14.png|350px]][[Image:Lung_cancer_UMR_tumor_haplotype_load_31Aug14.png|350px]][[Image:Pancreatic_cancer_UMR_tumor_haplotype_load_31Aug14.png|350px]] [[Image:CC_LC_PC_common_Go_biological_process_31Aug14.png|1200px]] [[Image:CC_LC_PC_common_Go_molecular_function_31Aug14.png|1200px]] [[Image:CC_LC_PC_common_InterPro_31Aug14.png|800px]] [[Image:CC_LC_PC_common_MSigDB_cancer_neighborhood_31Aug14.png|800px]]
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