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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

 
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