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===Inspect individual regions=== *Prepare two sampleInfo files for UCSD-004-05 and UCSD-004-07. *Report all regions in which HMHs were present in both tumor and matched plasma, but absence in normal plasma. ./report_tumor_HMH_regions.pl [[Media:UCSD-004-05_sampleInfo.txt|UCSD-004-05_sampleInfo.txt]] | sort -k 3nr > UCSD-004-05_HMH_regions.txt ./report_tumor_HMH_regions.pl [[Media:UCSD-004-07_sampleInfo.txt|UCSD-004-07_sampleInfo.txt]] | sort -k 3nr > UCSD-004-07_HMH_regions.txt *Then I picked individual regions and plotted methylation haplotypes in such regions. 1: Combined multiple hapInfo files cat s_1_1_ILMN_Indx04.hapInfo.txt s_1_1_ILMN_Indx05.hapInfo.txt s_1_2_ILMN_Indx04.hapInfo.txt s_1_2_ILMN_Indx05.hapInfo.txt > PC-T-2.pooled.hapInfo.txt cat s_2_1_ILMN_Indx02.hapInfo.txt s_2_2_ILMN_Indx02.hapInfo.txt > PC-P-2.pooled.hapInfo.txt cat s_2_1_ILMN_Indx14.hapInfo.txt s_2_2_ILMN_Indx14.hapInfo.txt s_2_1_ILMN_Indx15.hapInfo.txt s_2_2_ILMN_Indx15.hapInfo.txt s_2_1_ILMN_Indx16.hapInfo.txt s_2_2_ILMN_Indx16.hapInfo.txt s_2_1_ILMN_Indx27.hapInfo.txt s_2_2_ILMN_Indx27.hapInfo.txt NP-RRBS-NC-P-1ng-p2-Jun20-A013.hapInfo.txt > NC-plasma.pooled.hapInfo.txt 2: Prepare data files for plotting. ../prepare_plotting_files.pl NC-plasma.pooled.hapInfo.txt PC-T-2.pooled.hapInfo.txt PC-P-2.pooled.hapInfo.txt chr6:152128536-152129155 ../prepare_plotting_files.pl NC-plasma.pooled.hapInfo.txt PC-T-2.pooled.hapInfo.txt PC-P-2.pooled.hapInfo.txt chr5:176543913-176544076 3: Upload each "hapMatrix" file to [http://gattaca.imppc.org:3838/methylation_plotter/ Methylation-Plotter] to make a haplotype figure. chr6:152128536-152129155 (ESR1 promoter) Normal Plasma Primary Tumor Patient Plasma [[Image:chr6.152128536-152129155_hapMatrix_A.txt_main_plot_Mon_Jul_07_19_50_59_2014.png|300px]][[Image:chr6.152128536-152129155_hapMatrix_B.txt_main_plot_Mon_Jul_07_19_49_45_2014.png|400px]][[Image:chr6.152128536-152129155_hapMatrix_Mix.txt_main_plot_Mon_Jul_07_19_50_29_2014.png|300px]]
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