Description: A package of MATLAB code to normalize the peak intensity of ChIP-seq data and detect differential binding in the peaks. How to use: Change the parameters in MAnorm_run_through.m coordinately and run it under MATLAB to perform MAnorm on your ChIP-seq data. Output: (1) 4 figures of .tif and .fig (MATLAB figure) format that plot the M-A values before/after normalization, the P-value of differential binding and also the correlation between the log2-read densities of common peaks; (2) 2 .wig files that can be uploaded to genome browsers in order to visulize the M value of each peak; (3) 4 .xls files that describe the (M, A, P) values of each common/unique peak; (4) 3 .bed files that describe the genome coordinate and also M value of each non-differential and differential binding regions; Google Group: Please join our google group at http://groups.google.com/group/manorm for discussions. Example: We include the peaks from YALE ENCODE ChIP-seq data of cMYC in HelaS3 (replicate 1) and K562 (replicate 1) cells as a example in this package. If you download the raw data from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep1K562Cmyc.tagAlign.gz & http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2.tagAlign.gz and extract them to your local disk, then you will be able to run MAnorm to compare them as a example (remember to change the directories of the files in parameter region of MAnorm_run_through.m to The right ones). Below is the expected output in MATLAB: Step1: read peaks Start to read peak information: The tab-delimited bed file should have three, four or six columns with only one header line "Chromosom Start End Summit(relative to Start, Optional) Pvalue(Optional) FDR(Optional)" Hela_cMyc_rep1: 18924 peaks Start to read peak information: The tab-delimited bed file should have three, four or six columns with only one header line "Chromosom Start End Summit(relative to Start, Optional) Pvalue(Optional) FDR(Optional)" K562_cMyc_rep1: 13140 peaks Step2: classify common or unique peaks 12879 Hela_cMyc_rep1 unique peaks 7124 K562_cMyc_rep1 unique peaks 6045 Hela_cMyc_rep1 common peaks 6016 K562_cMyc_rep1 common peaks In random permutations, overlapping peaks: 96.73+/-9.7823 Fold change: 62.4935 Step3: read and split raw data by chromosome Start to split raw data file" The bed file should have exactly six columns "Chromosom Start End Any_Information Any_Information Strand" 100000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 200000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 300000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 400000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 500000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 600000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 700000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 800000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 900000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 1000000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 1100000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 1200000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 1300000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 1400000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 1500000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 1600000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 1700000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 1800000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 1900000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 2000000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 2100000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 2200000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 2300000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 2400000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 2500000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 2600000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 2700000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 2800000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 2900000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 3000000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 3100000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 3200000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 3300000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 3400000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 3500000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 3600000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 3700000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 3800000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 3900000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 4000000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 4100000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 4200000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 4300000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 4400000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 4500000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 4600000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 4700000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 4800000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 4900000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 5000000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 5100000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 5200000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 5300000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 5400000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 5500000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 5600000 reads splitted for marker wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 Start to split raw data file" The bed file should have exactly six columns "Chromosom Start End Any_Information Any_Information Strand" 100000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 200000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 300000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 400000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 500000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 600000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 700000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 800000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 900000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 1000000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 1100000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 1200000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 1300000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 1400000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 1500000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 1600000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 1700000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 1800000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 1900000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 2000000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 2100000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 2200000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 2300000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 2400000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 2500000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 2600000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 2700000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 2800000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 2900000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 3000000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 3100000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 3200000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 3300000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 3400000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 3500000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 3600000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 3700000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 3800000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 3900000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 4000000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 4100000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 4200000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 4300000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 4400000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 4500000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 4600000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 4700000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 4800000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 4900000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 5000000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 5100000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 5200000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 5300000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 5400000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 5500000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 5600000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 5700000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 5800000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 5900000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 6000000 reads splitted for marker Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 Step4: calculate read density in peaks marker_name = wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 TFname = Hela_cMyc_rep1_common reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr1 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr2 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr3 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr4 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr5 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr6 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr7 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr8 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr9 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr10 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr11 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr12 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr13 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr14 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr15 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr16 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr17 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr18 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr19 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr20 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr21 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr22 for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chrX for Hela_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chrY for Hela_cMyc_rep1_common peaks TFname = K562_cMyc_rep1_common reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr1 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr2 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr3 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr4 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr5 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr6 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr7 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr8 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr9 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr10 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr11 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr12 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr13 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr14 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr15 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr16 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr17 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr18 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr19 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr20 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr21 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr22 for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chrX for K562_cMyc_rep1_common peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chrY for K562_cMyc_rep1_common peaks TFname = Hela_cMyc_rep1_unique reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr1 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr2 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr3 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr4 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr5 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr6 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr7 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr8 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr9 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr10 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr11 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr12 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr13 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr14 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr15 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr16 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr17 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr18 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr19 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr20 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr21 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr22 for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chrX for Hela_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chrY for Hela_cMyc_rep1_unique peaks TFname = K562_cMyc_rep1_unique reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr1 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr2 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr3 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr4 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr5 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr6 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr7 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr8 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr9 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr10 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr11 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr12 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr13 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr14 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr15 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr16 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr17 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr18 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr19 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr20 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr21 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chr22 for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chrX for K562_cMyc_rep1_unique peaks reading reads of wgEncodeYaleChIPseqAlignmentsRep1Helas3CmycV2 on chrY for K562_cMyc_rep1_unique peaks marker_name = Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 TFname = Hela_cMyc_rep1_common reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr1 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr2 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr3 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr4 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr5 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr6 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr7 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr8 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr9 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr10 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr11 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr12 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr13 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr14 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr15 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr16 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr17 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr18 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr19 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr20 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr21 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr22 for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chrX for Hela_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chrY for Hela_cMyc_rep1_common peaks TFname = K562_cMyc_rep1_common reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr1 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr2 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr3 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr4 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr5 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr6 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr7 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr8 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr9 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr10 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr11 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr12 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr13 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr14 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr15 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr16 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr17 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr18 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr19 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr20 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr21 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr22 for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chrX for K562_cMyc_rep1_common peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chrY for K562_cMyc_rep1_common peaks TFname = Hela_cMyc_rep1_unique reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr1 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr2 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr3 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr4 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr5 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr6 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr7 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr8 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr9 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr10 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr11 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr12 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr13 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr14 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr15 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr16 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr17 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr18 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr19 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr20 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr21 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr22 for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chrX for Hela_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chrY for Hela_cMyc_rep1_unique peaks TFname = K562_cMyc_rep1_unique reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr1 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr2 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr3 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr4 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr5 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr6 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr7 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr8 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr9 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr10 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr11 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr12 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr13 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr14 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr15 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr16 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr17 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr18 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr19 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr20 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr21 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chr22 for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chrX for K562_cMyc_rep1_unique peaks reading reads of Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7 on chrY for K562_cMyc_rep1_unique peaks Final Step: normalize and output the M-A values Model for normalization: M = 0.57501 - 0.075466 * A Summarize data: output the M value of 2 peak sets to wig files Summarize data: merge common peaks and extract differential and non-differential binding regions Define sample 1 biased peaks from Hela_cMyc_rep1 peaks: 434 peaks with Fold Change>=2 are filtered from Hela_cMyc_rep1 common peaks 6556 peaks with Fold Change>=2 are filtered from Hela_cMyc_rep1 unique peaks In total, 6990 peaks with Fold Change>=2 are filtered from Hela_cMyc_rep1 peaks Define sample 2 biased peaks from K562_cMyc_rep1 peaks: 473 peaks with Fold Change<=-2 are filtered from K562_cMyc_rep1 common peaks 4621 peaks with Fold Change<=-2 are filtered from K562_cMyc_rep1 unique peaks In total, 5094 peaks with Fold Change<=-2 are filtered from K562_cMyc_rep1 peaks Define sample 1 and 2 unbiased peaks from Hela_cMyc_rep1 and K562_cMyc_rep1 peaks: 4775 peaks with |Fold Change|<2 are filtered from merged Hela_cMyc_rep1 and K562_cMyc_rep1 common peaks 3670 peaks with |Fold Change|<2 are filtered from Hela_cMyc_rep1 unique peaks 1835 peaks with |Fold Change|<2 are filtered from K562_cMyc_rep1 unique peaks In total, 10280 peaks with |Fold Change|<2 are filtered from Hela_cMyc_rep1 and K562_cMyc_rep1 peaks