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ChIPseq - Alignment and peak finding

Title: NS3143
Project: (none)
Started on: 9/15/2023 16:35:51
Hostname: login1.ufhpc
Run directory: /orange/licht/runs/NSD2-E1099K-Project/NS3143/NS3143
Configuration NS3143.conf
Table of contents:
  1. Input data
  2. Trimming and quality control
  3. Mapping to genome
  4. Genome coverage
  5. Peak detection (MACS2)
  6. Fraction of Reads in Peaks
  7. Differential peak analysis
  8. Peak detection (HOMER)
  9. Differential peak finding
  10. Motif finding
  11. MultiQC report
  12. UCSC hub
1. Input data
The following table summarizes the samples, conditions, and contrasts in this analysis. A readset is either a single fastq file or a pair of fastq files (for paired-end sequencing).

CategoryData
Summary of input data
Experimental conditions:NTKO-EZM-K27ac, NTKO-EZM-K27me3, NTKO-EZM-K36me2, NTKO-EZM-K36me3, NTKO-EZM-K4me1, NTKO-EZM-K4me3, NTKO-ctl-K27ac, NTKO-ctl-K27me3, NTKO-ctl-K36me2, NTKO-ctl-K36me3, NTKO-ctl-K4me1, NTKO-ctl-K4me3, TKO-EZM-K27ac, TKO-EZM-K27me3, TKO-EZM-K36me2, TKO-EZM-K36me3, TKO-EZM-K4me1, TKO-EZM-K4me3, TKO-ctl-K27ac, TKO-ctl-K27me3, TKO-ctl-K36me2, TKO-ctl-K36me3, TKO-ctl-K4me1, TKO-ctl-K4me3
Contrasts:NTKO-EZM-K27ac vs. NTKO-ctl-K27ac, TKO-EZM-K27ac vs. TKO-ctl-K27ac, TKO-ctl-K27ac vs. NTKO-ctl-K27ac, NTKO-EZM-K27me3 vs. NTKO-ctl-K27me3, TKO-EZM-K27me3 vs. TKO-ctl-K27me3, TKO-ctl-K27me3 vs. NTKO-ctl-K27me3, NTKO-EZM-K36me3 vs. NTKO-ctl-K36me3, TKO-EZM-K36me3 vs. TKO-ctl-K36me3, TKO-ctl-K36me3 vs. NTKO-ctl-K36me3, NTKO-EZM-K4me1 vs. NTKO-ctl-K4me1, TKO-EZM-K4me1 vs. TKO-ctl-K4me1, TKO-ctl-K4me1 vs. NTKO-ctl-K4me1, NTKO-EZM-K4me3 vs. NTKO-ctl-K4me3, TKO-EZM-K4me3 vs. TKO-ctl-K4me3, TKO-ctl-K4me3 vs. NTKO-ctl-K4me3, NTKO-EZM-K36me2 vs. NTKO-ctl-K36me2, TKO-EZM-K36me2 vs. TKO-ctl-K36me2, TKO-ctl-K36me2 vs. NTKO-ctl-K36me2
Number of samples24
Sequencing data data
Total number of reads:1,240,344,915
Average reads per sample:51,681,038
Table 1. Summary of input data



ConditionSampleNumber of reads% Reads
NTKO-EZM-K27acNTKO-EZM-K27ac-S101,196,0998.16%
NTKO-EZM-K27me3NTKO-EZM-K27me3-S52,762,5564.25%
NTKO-EZM-K36me2NTKO-EZM-K36me2-S56,677,7954.57%
NTKO-EZM-K36me3NTKO-EZM-K36me3-S63,202,2595.10%
NTKO-EZM-K4me1NTKO-EZM-K4me1-S43,447,7123.50%
NTKO-EZM-K4me3NTKO-EZM-K4me3-S56,781,8794.58%
NTKO-ctl-K27acNTKO-ctl-K27ac-S84,763,1496.83%
NTKO-ctl-K27me3NTKO-ctl-K27me3-S64,444,6915.20%
NTKO-ctl-K36me2NTKO-ctl-K36me2-S55,371,1244.46%
NTKO-ctl-K36me3NTKO-ctl-K36me3-S66,029,3255.32%
NTKO-ctl-K4me1NTKO-ctl-K4me1-S62,317,4315.02%
NTKO-ctl-K4me3NTKO-ctl-K4me3-S46,947,0993.79%
TKO-EZM-K27acTKO-EZM-K27ac-S56,075,2534.52%
TKO-EZM-K27me3TKO-EZM-K27me3-S45,379,9323.66%
TKO-EZM-K36me2TKO-EZM-K36me2-S16,591,2781.34%
TKO-EZM-K36me3TKO-EZM-K36me3-S74,175,4075.98%
TKO-EZM-K4me1TKO-EZM-K4me1-S16,549,1751.33%
TKO-EZM-K4me3TKO-EZM-K4me3-S41,890,6243.38%
TKO-ctl-K27acTKO-ctl-K27ac-S50,860,6554.10%
TKO-ctl-K27me3TKO-ctl-K27me3-S50,336,1204.06%
TKO-ctl-K36me2TKO-ctl-K36me2-S11,320,6230.91%
TKO-ctl-K36me3TKO-ctl-K36me3-S58,617,3234.73%
TKO-ctl-K4me1TKO-ctl-K4me1-S22,801,2711.84%
TKO-ctl-K4me3TKO-ctl-K4me3-S41,806,1353.37%
Table 2. Number of reads in each sample.

2. Trimming and quality control
The input sequences were trimmed using trimmomatic. Quality control was performed before and after trimming using FastQC. The following table provides links to the quality control reports before and after trimming, as well as the number of reads in the trimmed files.

SampleReadsetReads before trimQC before trimReads after trimQC after trim% Retained
NTKO-EZM-K27ac-SNTKO-EZM-K27ac-S_r1101,196,099NTKO-EZM-K27ac_S14_L004_R1_001
NTKO-EZM-K27ac_S14_L004_R2_001		97,486,982NTKO-EZM-K27ac_S14_L004_R1_001.trim.paired
NTKO-EZM-K27ac_S14_L004_R2_001.trim.paired		96.33%
NTKO-EZM-K27me3-SNTKO-EZM-K27me3-S_r152,762,556NTKO-EZM-K27me3_S18_L004_R1_001
NTKO-EZM-K27me3_S18_L004_R2_001		50,692,722NTKO-EZM-K27me3_S18_L004_R1_001.trim.paired
NTKO-EZM-K27me3_S18_L004_R2_001.trim.paired		96.08%
NTKO-EZM-K36me2-SNTKO-EZM-K36me2-S_r156,677,795NTKO-EZM-K36me2_S6_L004_R1_001
NTKO-EZM-K36me2_S6_L004_R2_001		54,775,823NTKO-EZM-K36me2_S6_L004_R1_001.trim.paired
NTKO-EZM-K36me2_S6_L004_R2_001.trim.paired		96.64%
NTKO-EZM-K36me3-SNTKO-EZM-K36me3-S_r163,202,259NTKO-EZM-K36me3_S22_L004_R1_001
NTKO-EZM-K36me3_S22_L004_R2_001		61,157,913NTKO-EZM-K36me3_S22_L004_R1_001.trim.paired
NTKO-EZM-K36me3_S22_L004_R2_001.trim.paired		96.77%
NTKO-EZM-K4me1-SNTKO-EZM-K4me1-S_r143,447,712NTKO-EZM-K4me1_S2_L004_R1_001
NTKO-EZM-K4me1_S2_L004_R2_001		41,962,092NTKO-EZM-K4me1_S2_L004_R1_001.trim.paired
NTKO-EZM-K4me1_S2_L004_R2_001.trim.paired		96.58%
NTKO-EZM-K4me3-SNTKO-EZM-K4me3-S_r156,781,879NTKO-EZM-K4me3_S10_L004_R1_001
NTKO-EZM-K4me3_S10_L004_R2_001		54,643,008NTKO-EZM-K4me3_S10_L004_R1_001.trim.paired
NTKO-EZM-K4me3_S10_L004_R2_001.trim.paired		96.23%
NTKO-ctl-K27ac-SNTKO-ctl-K27ac-S_r184,763,149NTKO-ctl-K27ac_S13_L004_R1_001
NTKO-ctl-K27ac_S13_L004_R2_001		81,801,737NTKO-ctl-K27ac_S13_L004_R1_001.trim.paired
NTKO-ctl-K27ac_S13_L004_R2_001.trim.paired		96.51%
NTKO-ctl-K27me3-SNTKO-ctl-K27me3-S_r164,444,691NTKO-ctl-K27me3_S17_L004_R1_001
NTKO-ctl-K27me3_S17_L004_R2_001		62,106,316NTKO-ctl-K27me3_S17_L004_R1_001.trim.paired
NTKO-ctl-K27me3_S17_L004_R2_001.trim.paired		96.37%
NTKO-ctl-K36me2-SNTKO-ctl-K36me2-S_r155,371,124NTKO-ctl-K36me2_S5_L004_R1_001
NTKO-ctl-K36me2_S5_L004_R2_001		53,641,628NTKO-ctl-K36me2_S5_L004_R1_001.trim.paired
NTKO-ctl-K36me2_S5_L004_R2_001.trim.paired		96.88%
NTKO-ctl-K36me3-SNTKO-ctl-K36me3-S_r166,029,325NTKO-ctl-K36me3_S21_L004_R1_001
NTKO-ctl-K36me3_S21_L004_R2_001		63,677,567NTKO-ctl-K36me3_S21_L004_R1_001.trim.paired
NTKO-ctl-K36me3_S21_L004_R2_001.trim.paired		96.44%
NTKO-ctl-K4me1-SNTKO-ctl-K4me1-S_r162,317,431NTKO-ctl-K4me1_S1_L004_R1_001
NTKO-ctl-K4me1_S1_L004_R2_001		60,019,067NTKO-ctl-K4me1_S1_L004_R1_001.trim.paired
NTKO-ctl-K4me1_S1_L004_R2_001.trim.paired		96.31%
NTKO-ctl-K4me3-SNTKO-ctl-K4me3-S_r146,947,099NTKO-ctl-K4me3_S9_L004_R1_001
NTKO-ctl-K4me3_S9_L004_R2_001		44,987,941NTKO-ctl-K4me3_S9_L004_R1_001.trim.paired
NTKO-ctl-K4me3_S9_L004_R2_001.trim.paired		95.83%
TKO-EZM-K27ac-STKO-EZM-K27ac-S_r156,075,253TKO-EZM-K27ac_S16_L004_R1_001
TKO-EZM-K27ac_S16_L004_R2_001		54,113,981TKO-EZM-K27ac_S16_L004_R1_001.trim.paired
TKO-EZM-K27ac_S16_L004_R2_001.trim.paired		96.50%
TKO-EZM-K27me3-STKO-EZM-K27me3-S_r145,379,932TKO-EZM-K27me3_S20_L004_R1_001
TKO-EZM-K27me3_S20_L004_R2_001		43,787,203TKO-EZM-K27me3_S20_L004_R1_001.trim.paired
TKO-EZM-K27me3_S20_L004_R2_001.trim.paired		96.49%
TKO-EZM-K36me2-STKO-EZM-K36me2-S_r116,591,278TKO-EZM-K36me2_S8_L004_R1_001
TKO-EZM-K36me2_S8_L004_R2_001		16,026,934TKO-EZM-K36me2_S8_L004_R1_001.trim.paired
TKO-EZM-K36me2_S8_L004_R2_001.trim.paired		96.60%
TKO-EZM-K36me3-STKO-EZM-K36me3-S_r174,175,407TKO-EZM-K36me3_S24_L004_R1_001
TKO-EZM-K36me3_S24_L004_R2_001		71,718,764TKO-EZM-K36me3_S24_L004_R1_001.trim.paired
TKO-EZM-K36me3_S24_L004_R2_001.trim.paired		96.69%
TKO-EZM-K4me1-STKO-EZM-K4me1-S_r116,549,175TKO-EZM-K4me1_S4_L004_R1_001
TKO-EZM-K4me1_S4_L004_R2_001		15,952,704TKO-EZM-K4me1_S4_L004_R1_001.trim.paired
TKO-EZM-K4me1_S4_L004_R2_001.trim.paired		96.40%
TKO-EZM-K4me3-STKO-EZM-K4me3-S_r141,890,624TKO-EZM-K4me3_S12_L004_R1_001
TKO-EZM-K4me3_S12_L004_R2_001		40,232,574TKO-EZM-K4me3_S12_L004_R1_001.trim.paired
TKO-EZM-K4me3_S12_L004_R2_001.trim.paired		96.04%
TKO-ctl-K27ac-STKO-ctl-K27ac-S_r150,860,655TKO-ctl-K27ac_S15_L004_R1_001
TKO-ctl-K27ac_S15_L004_R2_001		49,112,226TKO-ctl-K27ac_S15_L004_R1_001.trim.paired
TKO-ctl-K27ac_S15_L004_R2_001.trim.paired		96.56%
TKO-ctl-K27me3-STKO-ctl-K27me3-S_r150,336,120TKO-ctl-K27me3_S19_L004_R1_001
TKO-ctl-K27me3_S19_L004_R2_001		48,642,453TKO-ctl-K27me3_S19_L004_R1_001.trim.paired
TKO-ctl-K27me3_S19_L004_R2_001.trim.paired		96.64%
TKO-ctl-K36me2-STKO-ctl-K36me2-S_r111,320,623TKO-ctl-K36me2_S7_L004_R1_001
TKO-ctl-K36me2_S7_L004_R2_001		10,946,407TKO-ctl-K36me2_S7_L004_R1_001.trim.paired
TKO-ctl-K36me2_S7_L004_R2_001.trim.paired		96.69%
TKO-ctl-K36me3-STKO-ctl-K36me3-S_r158,617,323TKO-ctl-K36me3_S23_L004_R1_001
TKO-ctl-K36me3_S23_L004_R2_001		56,548,336TKO-ctl-K36me3_S23_L004_R1_001.trim.paired
TKO-ctl-K36me3_S23_L004_R2_001.trim.paired		96.47%
TKO-ctl-K4me1-STKO-ctl-K4me1-S_r122,801,271TKO-ctl-K4me1_S3_L004_R1_001
TKO-ctl-K4me1_S3_L004_R2_001		22,022,438TKO-ctl-K4me1_S3_L004_R1_001.trim.paired
TKO-ctl-K4me1_S3_L004_R2_001.trim.paired		96.58%
TKO-ctl-K4me3-STKO-ctl-K4me3-S_r141,806,135TKO-ctl-K4me3_S11_L004_R1_001
TKO-ctl-K4me3_S11_L004_R2_001		40,363,389TKO-ctl-K4me3_S11_L004_R1_001.trim.paired
TKO-ctl-K4me3_S11_L004_R2_001.trim.paired		96.55%
Table 3. Number of reads in input files and links to QC reports.

The following two tables report the number of reads before and after QC in each sample and in each condition.

SampleReads before QCReads after QC% Retained
NTKO-EZM-K27ac-S101,196,09997,486,98296.33%
NTKO-EZM-K27me3-S52,762,55650,692,72296.08%
NTKO-EZM-K36me2-S56,677,79554,775,82396.64%
NTKO-EZM-K36me3-S63,202,25961,157,91396.77%
NTKO-EZM-K4me1-S43,447,71241,962,09296.58%
NTKO-EZM-K4me3-S56,781,87954,643,00896.23%
NTKO-ctl-K27ac-S84,763,14981,801,73796.51%
NTKO-ctl-K27me3-S64,444,69162,106,31696.37%
NTKO-ctl-K36me2-S55,371,12453,641,62896.88%
NTKO-ctl-K36me3-S66,029,32563,677,56796.44%
NTKO-ctl-K4me1-S62,317,43160,019,06796.31%
NTKO-ctl-K4me3-S46,947,09944,987,94195.83%
TKO-EZM-K27ac-S56,075,25354,113,98196.50%
TKO-EZM-K27me3-S45,379,93243,787,20396.49%
TKO-EZM-K36me2-S16,591,27816,026,93496.60%
TKO-EZM-K36me3-S74,175,40771,718,76496.69%
TKO-EZM-K4me1-S16,549,17515,952,70496.40%
TKO-EZM-K4me3-S41,890,62440,232,57496.04%
TKO-ctl-K27ac-S50,860,65549,112,22696.56%
TKO-ctl-K27me3-S50,336,12048,642,45396.64%
TKO-ctl-K36me2-S11,320,62310,946,40796.69%
TKO-ctl-K36me3-S58,617,32356,548,33696.47%
TKO-ctl-K4me1-S22,801,27122,022,43896.58%
TKO-ctl-K4me3-S41,806,13540,363,38996.55%
Table 4. Number of reads in each sample before and after QC.



ConditionReads before QCReads after QC% Retained
NTKO-EZM-K27ac101,196,09997,486,98296.33%
NTKO-EZM-K27me352,762,55650,692,72296.08%
NTKO-EZM-K36me256,677,79554,775,82396.64%
NTKO-EZM-K36me363,202,25961,157,91396.77%
NTKO-EZM-K4me143,447,71241,962,09296.58%
NTKO-EZM-K4me356,781,87954,643,00896.23%
NTKO-ctl-K27ac84,763,14981,801,73796.51%
NTKO-ctl-K27me364,444,69162,106,31696.37%
NTKO-ctl-K36me255,371,12453,641,62896.88%
NTKO-ctl-K36me366,029,32563,677,56796.44%
NTKO-ctl-K4me162,317,43160,019,06796.31%
NTKO-ctl-K4me346,947,09944,987,94195.83%
TKO-EZM-K27ac56,075,25354,113,98196.50%
TKO-EZM-K27me345,379,93243,787,20396.49%
TKO-EZM-K36me216,591,27816,026,93496.60%
TKO-EZM-K36me374,175,40771,718,76496.69%
TKO-EZM-K4me116,549,17515,952,70496.40%
TKO-EZM-K4me341,890,62440,232,57496.04%
TKO-ctl-K27ac50,860,65549,112,22696.56%
TKO-ctl-K27me350,336,12048,642,45396.64%
TKO-ctl-K36me211,320,62310,946,40796.69%
TKO-ctl-K36me358,617,32356,548,33696.47%
TKO-ctl-K4me122,801,27122,022,43896.58%
TKO-ctl-K4me341,806,13540,363,38996.55%
Table 5. Number of reads in each condition before and after QC.

3. Mapping to genome
The input sequences were aligned to the genome using Bowtie 2.4.5. The following table reports the number of aligned reads for each sample. The WIG files can be uploaded to the UCSC Genome Browser as custom tracks.

SampleTotal readsAligned readsConcordant alignment rateBowtie2 report
NTKO-EZM-K27ac-S97,486,98280,003,71882.07%bam.bowtie/NTKO-EZM-K27ac-S.bt2stats.html
NTKO-EZM-K27me3-S50,692,72238,854,13676.65%bam.bowtie/NTKO-EZM-K27me3-S.bt2stats.html
NTKO-EZM-K36me2-S54,775,82344,631,66081.48%bam.bowtie/NTKO-EZM-K36me2-S.bt2stats.html
NTKO-EZM-K36me3-S61,157,91345,676,27474.69%bam.bowtie/NTKO-EZM-K36me3-S.bt2stats.html
NTKO-EZM-K4me1-S41,962,09234,497,82582.21%bam.bowtie/NTKO-EZM-K4me1-S.bt2stats.html
NTKO-EZM-K4me3-S54,643,00844,269,01581.01%bam.bowtie/NTKO-EZM-K4me3-S.bt2stats.html
NTKO-ctl-K27ac-S81,801,73768,486,53683.72%bam.bowtie/NTKO-ctl-K27ac-S.bt2stats.html
NTKO-ctl-K27me3-S62,106,31647,977,53577.25%bam.bowtie/NTKO-ctl-K27me3-S.bt2stats.html
NTKO-ctl-K36me2-S53,641,62844,460,36782.88%bam.bowtie/NTKO-ctl-K36me2-S.bt2stats.html
NTKO-ctl-K36me3-S63,677,56750,301,94878.99%bam.bowtie/NTKO-ctl-K36me3-S.bt2stats.html
NTKO-ctl-K4me1-S60,019,06749,909,18983.16%bam.bowtie/NTKO-ctl-K4me1-S.bt2stats.html
NTKO-ctl-K4me3-S44,987,94136,835,07281.88%bam.bowtie/NTKO-ctl-K4me3-S.bt2stats.html
TKO-EZM-K27ac-S54,113,98144,805,93782.80%bam.bowtie/TKO-EZM-K27ac-S.bt2stats.html
TKO-EZM-K27me3-S43,787,20335,083,52280.12%bam.bowtie/TKO-EZM-K27me3-S.bt2stats.html
TKO-EZM-K36me2-S16,026,93413,316,06283.09%bam.bowtie/TKO-EZM-K36me2-S.bt2stats.html
TKO-EZM-K36me3-S71,718,76452,955,99373.84%bam.bowtie/TKO-EZM-K36me3-S.bt2stats.html
TKO-EZM-K4me1-S15,952,70412,944,04581.14%bam.bowtie/TKO-EZM-K4me1-S.bt2stats.html
TKO-EZM-K4me3-S40,232,57433,016,77582.06%bam.bowtie/TKO-EZM-K4me3-S.bt2stats.html
TKO-ctl-K27ac-S49,112,22640,951,10683.38%bam.bowtie/TKO-ctl-K27ac-S.bt2stats.html
TKO-ctl-K27me3-S48,642,45339,407,92681.02%bam.bowtie/TKO-ctl-K27me3-S.bt2stats.html
TKO-ctl-K36me2-S10,946,4079,006,03882.27%bam.bowtie/TKO-ctl-K36me2-S.bt2stats.html
TKO-ctl-K36me3-S56,548,33644,983,72579.55%bam.bowtie/TKO-ctl-K36me3-S.bt2stats.html
TKO-ctl-K4me1-S22,022,43818,069,78482.05%bam.bowtie/TKO-ctl-K4me1-S.bt2stats.html
TKO-ctl-K4me3-S40,363,38933,378,80582.70%bam.bowtie/TKO-ctl-K4me3-S.bt2stats.html
Table 6. Number of alignments to genome.

4. Genome coverage
The following table reports the overall and effective genome coverage in each sample. The Total nt column reports the total number of nucleotides sequenced, i.e. the number of aligned reads times the length of each read. Coverage is this number divided by the size of the genome. Effective bp reports the number of bases in the genome having coverage greater than 5, and the Effective Perc column shows what percentage this is of the genome size. Note that, especially in the case of RNA-seq, the effective genome size may be much smaller than the full size. Eff Coverage is the average coverage over the effectively covered fraction of the genome.

NameTotal ntCoverageEffective bpEffective PercEff Coverage
NTKO-EZM-K27ac-S475,564,5310.1535,683,0271.20%13.33
NTKO-EZM-K27me3-S271,106,0140.0920,987,6830.70%12.92
NTKO-EZM-K36me2-S198,947,0220.0616,625,1910.50%11.97
NTKO-EZM-K36me3-S439,126,4800.1433,389,2681.10%13.15
NTKO-EZM-K4me1-S184,485,1560.0615,801,5700.50%11.68
NTKO-EZM-K4me3-S231,436,4790.0719,389,4790.60%11.94
NTKO-ctl-K27ac-S825,269,5050.2758,327,6831.90%14.15
NTKO-ctl-K27me3-S129,995,1960.049,137,7850.30%14.23
NTKO-ctl-K36me2-S194,361,0910.0616,507,6760.50%11.77
NTKO-ctl-K36me3-S298,294,2040.1024,230,0560.80%12.31
NTKO-ctl-K4me1-S314,618,4390.1028,760,1440.90%10.94
NTKO-ctl-K4me3-S406,131,1490.1326,658,4360.90%15.23
TKO-EZM-K27ac-S822,449,3230.2756,676,5671.80%14.51
TKO-EZM-K27me3-S108,834,5160.048,296,8170.30%13.12
TKO-EZM-K36me2-S17,443,3200.011,419,6230.00%12.29
TKO-EZM-K36me3-S486,516,5190.1637,947,0511.20%12.82
TKO-EZM-K4me1-S29,211,4290.012,083,3750.10%14.02
TKO-EZM-K4me3-S175,278,1220.0614,923,1710.50%11.75
TKO-ctl-K27ac-S410,136,4170.1331,232,5171.00%13.13
TKO-ctl-K27me3-S120,457,4850.049,284,9840.30%12.97
TKO-ctl-K36me2-S14,706,6060.001,030,7240.00%14.27
TKO-ctl-K36me3-S376,634,3830.1234,489,2281.10%10.92
TKO-ctl-K4me1-S42,207,4240.013,156,5840.10%13.37
TKO-ctl-K4me3-S223,542,1980.0718,230,4170.60%12.26
Table 7. Genome coverage by sample.

The following table reports the overall and effective genome coverage in each condition.

NameTotal ntCoverageEffective bpEffective PercEff Coverage
NTKO-EZM-K27ac475,564,5310.1535,683,0271.20%13.33
NTKO-EZM-K27me3271,106,0140.0920,987,6830.70%12.92
NTKO-EZM-K36me2198,947,0220.0616,625,1910.50%11.97
NTKO-EZM-K36me3439,126,4800.1433,389,2681.10%13.15
NTKO-EZM-K4me1184,485,1560.0615,801,5700.50%11.68
NTKO-EZM-K4me3231,436,4790.0719,389,4790.60%11.94
NTKO-ctl-K27ac825,269,5050.2758,327,6831.90%14.15
NTKO-ctl-K27me3129,995,1960.049,137,7850.30%14.23
NTKO-ctl-K36me2194,361,0910.0616,507,6760.50%11.77
NTKO-ctl-K36me3298,294,2040.1024,230,0560.80%12.31
NTKO-ctl-K4me1314,618,4390.1028,760,1440.90%10.94
NTKO-ctl-K4me3406,131,1490.1326,658,4360.90%15.23
TKO-EZM-K27ac822,449,3230.2756,676,5671.80%14.51
TKO-EZM-K27me3108,834,5160.048,296,8170.30%13.12
TKO-EZM-K36me217,443,3200.011,419,6230.00%12.29
TKO-EZM-K36me3486,516,5190.1637,947,0511.20%12.82
TKO-EZM-K4me129,211,4290.012,083,3750.10%14.02
TKO-EZM-K4me3175,278,1220.0614,923,1710.50%11.75
TKO-ctl-K27ac410,136,4170.1331,232,5171.00%13.13
TKO-ctl-K27me3120,457,4850.049,284,9840.30%12.97
TKO-ctl-K36me214,706,6060.001,030,7240.00%14.27
TKO-ctl-K36me3376,634,3830.1234,489,2281.10%10.92
TKO-ctl-K4me142,207,4240.013,156,5840.10%13.37
TKO-ctl-K4me3223,542,1980.0718,230,4170.60%12.26
Table 8. Genome coverage by condition

File: NS3143.sample.cov.xlsx
Size: 57.99 kB
Description: Per-chromosome coverage data, by sample.

File: NS3143.cond.cov.xlsx
Size: 57.98 kB
Description: Per-chromosome coverage data, by condition.

5. Peak detection (MACS2)
Peak detection was performed using MACS version 2.2.7.1 with the following options: broad=N, model=Y, paired=Y, qvalue=0.05. The following table shows the number of peaks found for each condition, and their classification. Click on the link in the Peaks column to download the list of peaks in tab-delimited format.

ConditionTotal PeaksPeaksActions
NTKO-EZM-K27ac44,694NTKO-EZM-K27ac.macs/NTKO-EZM-K27ac_peaks.csvCreate RegionSet
NTKO-EZM-K27me343,709NTKO-EZM-K27me3.macs/NTKO-EZM-K27me3_peaks.csvCreate RegionSet
NTKO-EZM-K36me228,116NTKO-EZM-K36me2.macs/NTKO-EZM-K36me2_peaks.csvCreate RegionSet
NTKO-EZM-K36me330,826NTKO-EZM-K36me3.macs/NTKO-EZM-K36me3_peaks.csvCreate RegionSet
NTKO-EZM-K4me137,255NTKO-EZM-K4me1.macs/NTKO-EZM-K4me1_peaks.csvCreate RegionSet
NTKO-EZM-K4me338,628NTKO-EZM-K4me3.macs/NTKO-EZM-K4me3_peaks.csvCreate RegionSet
NTKO-ctl-K27ac51,922NTKO-ctl-K27ac.macs/NTKO-ctl-K27ac_peaks.csvCreate RegionSet
NTKO-ctl-K27me330,895NTKO-ctl-K27me3.macs/NTKO-ctl-K27me3_peaks.csvCreate RegionSet
NTKO-ctl-K36me228,670NTKO-ctl-K36me2.macs/NTKO-ctl-K36me2_peaks.csvCreate RegionSet
NTKO-ctl-K36me326,825NTKO-ctl-K36me3.macs/NTKO-ctl-K36me3_peaks.csvCreate RegionSet
NTKO-ctl-K4me133,749NTKO-ctl-K4me1.macs/NTKO-ctl-K4me1_peaks.csvCreate RegionSet
NTKO-ctl-K4me343,249NTKO-ctl-K4me3.macs/NTKO-ctl-K4me3_peaks.csvCreate RegionSet
TKO-EZM-K27ac66,215TKO-EZM-K27ac.macs/TKO-EZM-K27ac_peaks.csvCreate RegionSet
TKO-EZM-K27me321,890TKO-EZM-K27me3.macs/TKO-EZM-K27me3_peaks.csvCreate RegionSet
TKO-EZM-K36me226,049TKO-EZM-K36me2.macs/TKO-EZM-K36me2_peaks.csvCreate RegionSet
TKO-EZM-K36me325,080TKO-EZM-K36me3.macs/TKO-EZM-K36me3_peaks.csvCreate RegionSet
TKO-EZM-K4me113,355TKO-EZM-K4me1.macs/TKO-EZM-K4me1_peaks.csvCreate RegionSet
TKO-EZM-K4me330,270TKO-EZM-K4me3.macs/TKO-EZM-K4me3_peaks.csvCreate RegionSet
TKO-ctl-K27ac42,600TKO-ctl-K27ac.macs/TKO-ctl-K27ac_peaks.csvCreate RegionSet
TKO-ctl-K27me323,048TKO-ctl-K27me3.macs/TKO-ctl-K27me3_peaks.csvCreate RegionSet
TKO-ctl-K36me221,102TKO-ctl-K36me2.macs/TKO-ctl-K36me2_peaks.csvCreate RegionSet
TKO-ctl-K36me345,897TKO-ctl-K36me3.macs/TKO-ctl-K36me3_peaks.csvCreate RegionSet
TKO-ctl-K4me117,352TKO-ctl-K4me1.macs/TKO-ctl-K4me1_peaks.csvCreate RegionSet
TKO-ctl-K4me336,745TKO-ctl-K4me3.macs/TKO-ctl-K4me3_peaks.csvCreate RegionSet
Table 9. Classification of peaks in genome regions

The following table provides links to the Pileup, narrowPeaks, and Summits files for each condition. All files are in bedGraph format.

ConditionNum peaksPileupPeaksSummits
NTKO-EZM-K27ac44,694NTKO-EZM-K27ac.macs/NTKO-EZM-K27ac.bedGraphNTKO-EZM-K27ac.macs/NTKO-EZM-K27ac.npeaks.bedGraphNTKO-EZM-K27ac.macs/NTKO-EZM-K27ac.summits.bedGraph
NTKO-EZM-K27me343,709NTKO-EZM-K27me3.macs/NTKO-EZM-K27me3.bedGraphNTKO-EZM-K27me3.macs/NTKO-EZM-K27me3.npeaks.bedGraphNTKO-EZM-K27me3.macs/NTKO-EZM-K27me3.summits.bedGraph
NTKO-EZM-K36me228,116NTKO-EZM-K36me2.macs/NTKO-EZM-K36me2.bedGraphNTKO-EZM-K36me2.macs/NTKO-EZM-K36me2.npeaks.bedGraphNTKO-EZM-K36me2.macs/NTKO-EZM-K36me2.summits.bedGraph
NTKO-EZM-K36me330,826NTKO-EZM-K36me3.macs/NTKO-EZM-K36me3.bedGraphNTKO-EZM-K36me3.macs/NTKO-EZM-K36me3.npeaks.bedGraphNTKO-EZM-K36me3.macs/NTKO-EZM-K36me3.summits.bedGraph
NTKO-EZM-K4me137,255NTKO-EZM-K4me1.macs/NTKO-EZM-K4me1.bedGraphNTKO-EZM-K4me1.macs/NTKO-EZM-K4me1.npeaks.bedGraphNTKO-EZM-K4me1.macs/NTKO-EZM-K4me1.summits.bedGraph
NTKO-EZM-K4me338,628NTKO-EZM-K4me3.macs/NTKO-EZM-K4me3.bedGraphNTKO-EZM-K4me3.macs/NTKO-EZM-K4me3.npeaks.bedGraphNTKO-EZM-K4me3.macs/NTKO-EZM-K4me3.summits.bedGraph
NTKO-ctl-K27ac51,922NTKO-ctl-K27ac.macs/NTKO-ctl-K27ac.bedGraphNTKO-ctl-K27ac.macs/NTKO-ctl-K27ac.npeaks.bedGraphNTKO-ctl-K27ac.macs/NTKO-ctl-K27ac.summits.bedGraph
NTKO-ctl-K27me330,895NTKO-ctl-K27me3.macs/NTKO-ctl-K27me3.bedGraphNTKO-ctl-K27me3.macs/NTKO-ctl-K27me3.npeaks.bedGraphNTKO-ctl-K27me3.macs/NTKO-ctl-K27me3.summits.bedGraph
NTKO-ctl-K36me228,670NTKO-ctl-K36me2.macs/NTKO-ctl-K36me2.bedGraphNTKO-ctl-K36me2.macs/NTKO-ctl-K36me2.npeaks.bedGraphNTKO-ctl-K36me2.macs/NTKO-ctl-K36me2.summits.bedGraph
NTKO-ctl-K36me326,825NTKO-ctl-K36me3.macs/NTKO-ctl-K36me3.bedGraphNTKO-ctl-K36me3.macs/NTKO-ctl-K36me3.npeaks.bedGraphNTKO-ctl-K36me3.macs/NTKO-ctl-K36me3.summits.bedGraph
NTKO-ctl-K4me133,749NTKO-ctl-K4me1.macs/NTKO-ctl-K4me1.bedGraphNTKO-ctl-K4me1.macs/NTKO-ctl-K4me1.npeaks.bedGraphNTKO-ctl-K4me1.macs/NTKO-ctl-K4me1.summits.bedGraph
NTKO-ctl-K4me343,249NTKO-ctl-K4me3.macs/NTKO-ctl-K4me3.bedGraphNTKO-ctl-K4me3.macs/NTKO-ctl-K4me3.npeaks.bedGraphNTKO-ctl-K4me3.macs/NTKO-ctl-K4me3.summits.bedGraph
TKO-EZM-K27ac66,215TKO-EZM-K27ac.macs/TKO-EZM-K27ac.bedGraphTKO-EZM-K27ac.macs/TKO-EZM-K27ac.npeaks.bedGraphTKO-EZM-K27ac.macs/TKO-EZM-K27ac.summits.bedGraph
TKO-EZM-K27me321,890TKO-EZM-K27me3.macs/TKO-EZM-K27me3.bedGraphTKO-EZM-K27me3.macs/TKO-EZM-K27me3.npeaks.bedGraphTKO-EZM-K27me3.macs/TKO-EZM-K27me3.summits.bedGraph
TKO-EZM-K36me226,049TKO-EZM-K36me2.macs/TKO-EZM-K36me2.bedGraphTKO-EZM-K36me2.macs/TKO-EZM-K36me2.npeaks.bedGraphTKO-EZM-K36me2.macs/TKO-EZM-K36me2.summits.bedGraph
TKO-EZM-K36me325,080TKO-EZM-K36me3.macs/TKO-EZM-K36me3.bedGraphTKO-EZM-K36me3.macs/TKO-EZM-K36me3.npeaks.bedGraphTKO-EZM-K36me3.macs/TKO-EZM-K36me3.summits.bedGraph
TKO-EZM-K4me113,355TKO-EZM-K4me1.macs/TKO-EZM-K4me1.bedGraphTKO-EZM-K4me1.macs/TKO-EZM-K4me1.npeaks.bedGraphTKO-EZM-K4me1.macs/TKO-EZM-K4me1.summits.bedGraph
TKO-EZM-K4me330,270TKO-EZM-K4me3.macs/TKO-EZM-K4me3.bedGraphTKO-EZM-K4me3.macs/TKO-EZM-K4me3.npeaks.bedGraphTKO-EZM-K4me3.macs/TKO-EZM-K4me3.summits.bedGraph
TKO-ctl-K27ac42,600TKO-ctl-K27ac.macs/TKO-ctl-K27ac.bedGraphTKO-ctl-K27ac.macs/TKO-ctl-K27ac.npeaks.bedGraphTKO-ctl-K27ac.macs/TKO-ctl-K27ac.summits.bedGraph
TKO-ctl-K27me323,048TKO-ctl-K27me3.macs/TKO-ctl-K27me3.bedGraphTKO-ctl-K27me3.macs/TKO-ctl-K27me3.npeaks.bedGraphTKO-ctl-K27me3.macs/TKO-ctl-K27me3.summits.bedGraph
TKO-ctl-K36me221,102TKO-ctl-K36me2.macs/TKO-ctl-K36me2.bedGraphTKO-ctl-K36me2.macs/TKO-ctl-K36me2.npeaks.bedGraphTKO-ctl-K36me2.macs/TKO-ctl-K36me2.summits.bedGraph
TKO-ctl-K36me345,897TKO-ctl-K36me3.macs/TKO-ctl-K36me3.bedGraphTKO-ctl-K36me3.macs/TKO-ctl-K36me3.npeaks.bedGraphTKO-ctl-K36me3.macs/TKO-ctl-K36me3.summits.bedGraph
TKO-ctl-K4me117,352TKO-ctl-K4me1.macs/TKO-ctl-K4me1.bedGraphTKO-ctl-K4me1.macs/TKO-ctl-K4me1.npeaks.bedGraphTKO-ctl-K4me1.macs/TKO-ctl-K4me1.summits.bedGraph
TKO-ctl-K4me336,745TKO-ctl-K4me3.macs/TKO-ctl-K4me3.bedGraphTKO-ctl-K4me3.macs/TKO-ctl-K4me3.npeaks.bedGraphTKO-ctl-K4me3.macs/TKO-ctl-K4me3.summits.bedGraph
Table 10. Results of peak detection with MACS.

The following histogram shows the distribution of peak locations in the different conditions.
6. Fraction of Reads in Peaks
The Fraction of Reads in Peaks (FRIP) is the fraction of reads that fall in regions called as peaks, out of all aligned peaks.

ConditionReadsReads in peaksFRIP
NTKO-EZM-K27ac183,167,43551,272,52827.99%
NTKO-EZM-K27me392,967,38811,057,90211.89%
NTKO-EZM-K36me2105,519,3274,240,4924.02%
NTKO-EZM-K36me3111,314,9005,969,6405.36%
NTKO-EZM-K4me181,419,9604,463,6695.48%
NTKO-EZM-K4me3102,024,28435,869,51735.16%
NTKO-ctl-K27ac157,224,74939,505,66725.13%
NTKO-ctl-K27me3114,562,2239,894,1088.64%
NTKO-ctl-K36me2104,994,1424,097,4083.90%
NTKO-ctl-K36me3119,811,0156,176,6035.16%
NTKO-ctl-K4me1117,303,9336,047,0485.16%
NTKO-ctl-K4me384,707,93633,876,97939.99%
TKO-EZM-K27ac102,588,26030,606,81829.83%
TKO-EZM-K27me382,456,9223,285,9223.99%
TKO-EZM-K36me231,262,7661,778,8205.69%
TKO-EZM-K36me3128,160,1336,263,9444.89%
TKO-EZM-K4me130,709,181735,5822.40%
TKO-EZM-K4me375,286,56829,453,82539.12%
TKO-ctl-K27ac93,404,07726,225,27128.08%
TKO-ctl-K27me392,478,6413,767,1344.07%
TKO-ctl-K36me221,213,1571,108,2855.22%
TKO-ctl-K36me3106,363,92110,739,61910.10%
TKO-ctl-K4me142,732,8431,280,1183.00%
TKO-ctl-K4me376,896,06124,968,76232.47%
Table 11. Fraction of Reads in Peaks

7. Differential peak analysis
For each contrast, peaks in the two conditions were compared to identify those appearing in only the test or the control, or those significantly higher in the test than in the control (abs(log2(FC)) > 1). The following table reports the number of peaks identified in each group.

TestControlTest upControl upUnchanged
NTKO-EZM-K27acNTKO-ctl-K27acNTKO-EZM-K27ac.vs.NTKO-ctl-K27ac.testup.bed (8,756)NTKO-EZM-K27ac.vs.NTKO-ctl-K27ac.ctrlup.bed (2,492)NTKO-EZM-K27ac.vs.NTKO-ctl-K27ac.commpeaks.bed (44,694)
TKO-EZM-K27acTKO-ctl-K27acTKO-EZM-K27ac.vs.TKO-ctl-K27ac.testup.bed (17,236)TKO-EZM-K27ac.vs.TKO-ctl-K27ac.ctrlup.bed (2,768)TKO-EZM-K27ac.vs.TKO-ctl-K27ac.commpeaks.bed (66,215)
TKO-ctl-K27acNTKO-ctl-K27acTKO-ctl-K27ac.vs.NTKO-ctl-K27ac.testup.bed (11,925)TKO-ctl-K27ac.vs.NTKO-ctl-K27ac.ctrlup.bed (2,105)TKO-ctl-K27ac.vs.NTKO-ctl-K27ac.commpeaks.bed (42,600)
NTKO-EZM-K27me3NTKO-ctl-K27me3NTKO-EZM-K27me3.vs.NTKO-ctl-K27me3.testup.bed (15,345)NTKO-EZM-K27me3.vs.NTKO-ctl-K27me3.ctrlup.bed (2,974)NTKO-EZM-K27me3.vs.NTKO-ctl-K27me3.commpeaks.bed (43,709)
TKO-EZM-K27me3TKO-ctl-K27me3TKO-EZM-K27me3.vs.TKO-ctl-K27me3.testup.bed (5,909)TKO-EZM-K27me3.vs.TKO-ctl-K27me3.ctrlup.bed (1,696)TKO-EZM-K27me3.vs.TKO-ctl-K27me3.commpeaks.bed (21,890)
TKO-ctl-K27me3NTKO-ctl-K27me3TKO-ctl-K27me3.vs.NTKO-ctl-K27me3.testup.bed (6,467)TKO-ctl-K27me3.vs.NTKO-ctl-K27me3.ctrlup.bed (2,050)TKO-ctl-K27me3.vs.NTKO-ctl-K27me3.commpeaks.bed (23,048)
NTKO-EZM-K36me3NTKO-ctl-K36me3NTKO-EZM-K36me3.vs.NTKO-ctl-K36me3.testup.bed (10,612)NTKO-EZM-K36me3.vs.NTKO-ctl-K36me3.ctrlup.bed (2,689)NTKO-EZM-K36me3.vs.NTKO-ctl-K36me3.commpeaks.bed (30,826)
TKO-EZM-K36me3TKO-ctl-K36me3TKO-EZM-K36me3.vs.TKO-ctl-K36me3.testup.bed (7,516)TKO-EZM-K36me3.vs.TKO-ctl-K36me3.ctrlup.bed (2,392)TKO-EZM-K36me3.vs.TKO-ctl-K36me3.commpeaks.bed (25,080)
TKO-ctl-K36me3NTKO-ctl-K36me3TKO-ctl-K36me3.vs.NTKO-ctl-K36me3.testup.bed (18,269)TKO-ctl-K36me3.vs.NTKO-ctl-K36me3.ctrlup.bed (2,639)TKO-ctl-K36me3.vs.NTKO-ctl-K36me3.commpeaks.bed (45,897)
NTKO-EZM-K4me1NTKO-ctl-K4me1NTKO-EZM-K4me1.vs.NTKO-ctl-K4me1.testup.bed (12,491)NTKO-EZM-K4me1.vs.NTKO-ctl-K4me1.ctrlup.bed (2,740)NTKO-EZM-K4me1.vs.NTKO-ctl-K4me1.commpeaks.bed (37,255)
TKO-EZM-K4me1TKO-ctl-K4me1TKO-EZM-K4me1.vs.TKO-ctl-K4me1.testup.bed (3,019)TKO-EZM-K4me1.vs.TKO-ctl-K4me1.ctrlup.bed (763)TKO-EZM-K4me1.vs.TKO-ctl-K4me1.commpeaks.bed (13,355)
TKO-ctl-K4me1NTKO-ctl-K4me1TKO-ctl-K4me1.vs.NTKO-ctl-K4me1.testup.bed (4,028)TKO-ctl-K4me1.vs.NTKO-ctl-K4me1.ctrlup.bed (2,012)TKO-ctl-K4me1.vs.NTKO-ctl-K4me1.commpeaks.bed (17,352)
NTKO-EZM-K4me3NTKO-ctl-K4me3NTKO-EZM-K4me3.vs.NTKO-ctl-K4me3.testup.bed (5,859)NTKO-EZM-K4me3.vs.NTKO-ctl-K4me3.ctrlup.bed (1,959)NTKO-EZM-K4me3.vs.NTKO-ctl-K4me3.commpeaks.bed (38,628)
TKO-EZM-K4me3TKO-ctl-K4me3TKO-EZM-K4me3.vs.TKO-ctl-K4me3.testup.bed (6,558)TKO-EZM-K4me3.vs.TKO-ctl-K4me3.ctrlup.bed (1,057)TKO-EZM-K4me3.vs.TKO-ctl-K4me3.commpeaks.bed (30,270)
TKO-ctl-K4me3NTKO-ctl-K4me3TKO-ctl-K4me3.vs.NTKO-ctl-K4me3.testup.bed (5,960)TKO-ctl-K4me3.vs.NTKO-ctl-K4me3.ctrlup.bed (2,150)TKO-ctl-K4me3.vs.NTKO-ctl-K4me3.commpeaks.bed (36,745)
NTKO-EZM-K36me2NTKO-ctl-K36me2NTKO-EZM-K36me2.vs.NTKO-ctl-K36me2.testup.bed (8,557)NTKO-EZM-K36me2.vs.NTKO-ctl-K36me2.ctrlup.bed (2,507)NTKO-EZM-K36me2.vs.NTKO-ctl-K36me2.commpeaks.bed (28,116)
TKO-EZM-K36me2TKO-ctl-K36me2TKO-EZM-K36me2.vs.TKO-ctl-K36me2.testup.bed (10,701)TKO-EZM-K36me2.vs.TKO-ctl-K36me2.ctrlup.bed (778)TKO-EZM-K36me2.vs.TKO-ctl-K36me2.commpeaks.bed (26,049)
TKO-ctl-K36me2NTKO-ctl-K36me2TKO-ctl-K36me2.vs.NTKO-ctl-K36me2.testup.bed (9,270)TKO-ctl-K36me2.vs.NTKO-ctl-K36me2.ctrlup.bed (1,806)TKO-ctl-K36me2.vs.NTKO-ctl-K36me2.commpeaks.bed (21,102)
Table 12. Number of differentially expressed peaks in each contrast.

The following table reports the classification of the number of differentially expressed peaks by gene region in all contrasts.

TestControlGroupUpstreamExonCodingExonIntronDownstreamIntergenic
NTKO-EZM-K27acNTKO-ctl-K27acTest up13.51%7.77%2.68%42.80%7.18%26.05%
NTKO-EZM-K27acNTKO-ctl-K27acControl up9.03%4.51%2.03%26.21%4.84%53.38%
NTKO-EZM-K27acNTKO-ctl-K27acCommon23.22%14.25%4.68%39.82%7.32%10.70%
TKO-EZM-K27acTKO-ctl-K27acTest up11.71%7.17%2.74%46.38%8.98%23.03%
TKO-EZM-K27acTKO-ctl-K27acControl up13.83%7.62%2.37%37.51%7.02%31.65%
TKO-EZM-K27acTKO-ctl-K27acCommon20.64%12.11%3.93%42.13%8.01%13.18%
TKO-ctl-K27acNTKO-ctl-K27acTest up14.45%8.45%3.14%46.26%8.10%19.61%
TKO-ctl-K27acNTKO-ctl-K27acControl up8.73%4.54%1.91%27.29%6.52%51.01%
TKO-ctl-K27acNTKO-ctl-K27acCommon24.47%13.80%4.49%39.80%7.58%9.87%
NTKO-EZM-K27me3NTKO-ctl-K27me3Test up9.67%6.19%3.14%39.98%8.67%32.34%
NTKO-EZM-K27me3NTKO-ctl-K27me3Control up6.85%3.30%1.55%29.82%6.09%52.40%
NTKO-EZM-K27me3NTKO-ctl-K27me3Common11.99%7.25%3.85%41.79%9.67%25.45%
TKO-EZM-K27me3TKO-ctl-K27me3Test up7.28%4.33%2.37%38.70%6.68%40.64%
TKO-EZM-K27me3TKO-ctl-K27me3Control up4.12%1.87%0.48%21.02%4.12%68.40%
TKO-EZM-K27me3TKO-ctl-K27me3Common10.85%5.51%3.18%42.09%8.36%30.00%
TKO-ctl-K27me3NTKO-ctl-K27me3Test up7.25%4.67%1.92%39.17%7.41%39.58%
TKO-ctl-K27me3NTKO-ctl-K27me3Control up4.75%2.29%1.68%21.87%3.84%65.57%
TKO-ctl-K27me3NTKO-ctl-K27me3Common10.94%5.95%2.85%40.58%9.70%29.98%
NTKO-EZM-K36me3NTKO-ctl-K36me3Test up4.78%2.84%1.21%36.73%4.53%49.91%
NTKO-EZM-K36me3NTKO-ctl-K36me3Control up5.25%3.59%2.27%27.94%6.26%54.69%
NTKO-EZM-K36me3NTKO-ctl-K36me3Common7.56%5.56%3.33%39.30%8.12%36.12%
TKO-EZM-K36me3TKO-ctl-K36me3Test up5.49%2.58%1.23%32.60%4.16%53.93%
TKO-EZM-K36me3TKO-ctl-K36me3Control up6.55%4.81%3.81%28.74%7.42%48.68%
TKO-EZM-K36me3TKO-ctl-K36me3Common8.87%5.22%3.21%39.72%7.28%35.71%
TKO-ctl-K36me3NTKO-ctl-K36me3Test up10.12%11.44%7.71%45.98%15.93%8.83%
TKO-ctl-K36me3NTKO-ctl-K36me3Control up4.24%2.76%1.18%22.12%4.83%64.87%
TKO-ctl-K36me3NTKO-ctl-K36me3Common10.32%12.88%9.14%44.15%17.08%6.42%
NTKO-EZM-K4me1NTKO-ctl-K4me1Test up9.17%7.08%3.53%44.62%10.10%25.49%
NTKO-EZM-K4me1NTKO-ctl-K4me1Control up5.68%2.42%1.24%27.37%5.16%58.12%
NTKO-EZM-K4me1NTKO-ctl-K4me1Common11.72%8.93%4.86%44.97%11.08%18.44%
TKO-EZM-K4me1TKO-ctl-K4me1Test up7.86%4.64%2.14%42.94%8.53%33.90%
TKO-EZM-K4me1TKO-ctl-K4me1Control up4.89%1.93%2.05%24.09%4.77%62.27%
TKO-EZM-K4me1TKO-ctl-K4me1Common7.37%4.29%2.68%43.03%8.18%34.45%
TKO-ctl-K4me1NTKO-ctl-K4me1Test up8.43%5.19%2.63%44.00%8.33%31.41%
TKO-ctl-K4me1NTKO-ctl-K4me1Control up3.78%1.69%1.51%20.90%3.47%68.65%
TKO-ctl-K4me1NTKO-ctl-K4me1Common10.12%4.96%3.46%39.78%8.88%32.79%
NTKO-EZM-K4me3NTKO-ctl-K4me3Test up16.00%7.75%2.46%41.13%8.41%24.25%
NTKO-EZM-K4me3NTKO-ctl-K4me3Control up21.12%9.92%3.36%29.00%5.93%30.68%
NTKO-EZM-K4me3NTKO-ctl-K4me3Common29.67%17.68%5.84%34.72%6.64%5.46%
TKO-EZM-K4me3TKO-ctl-K4me3Test up23.80%12.95%4.05%38.42%7.50%13.28%
TKO-EZM-K4me3TKO-ctl-K4me3Control up18.42%9.24%2.45%29.23%6.35%34.32%
TKO-EZM-K4me3TKO-ctl-K4me3Common30.14%18.45%5.98%34.32%6.33%4.79%
TKO-ctl-K4me3NTKO-ctl-K4me3Test up14.39%7.48%2.84%43.59%8.43%23.28%
TKO-ctl-K4me3NTKO-ctl-K4me3Control up23.50%12.97%3.78%31.42%5.10%23.22%
TKO-ctl-K4me3NTKO-ctl-K4me3Common29.49%18.46%5.85%34.13%6.60%5.47%
NTKO-EZM-K36me2NTKO-ctl-K36me2Test up6.08%4.35%1.79%41.87%7.14%38.76%
NTKO-EZM-K36me2NTKO-ctl-K36me2Control up4.17%1.55%1.17%25.26%4.24%63.62%
NTKO-EZM-K36me2NTKO-ctl-K36me2Common8.10%3.96%2.41%41.88%6.90%36.76%
TKO-EZM-K36me2TKO-ctl-K36me2Test up8.10%6.03%2.68%48.91%8.07%26.21%
TKO-EZM-K36me2TKO-ctl-K36me2Control up5.70%4.25%2.69%32.44%7.67%47.25%
TKO-EZM-K36me2TKO-ctl-K36me2Common9.03%6.51%3.19%48.77%8.66%23.83%
TKO-ctl-K36me2NTKO-ctl-K36me2Test up7.83%5.57%2.76%48.37%8.31%27.16%
TKO-ctl-K36me2NTKO-ctl-K36me2Control up3.56%1.60%0.95%20.75%3.91%69.22%
TKO-ctl-K36me2NTKO-ctl-K36me2Common8.76%4.12%3.38%45.72%7.50%30.52%
Table 13. Location of differential peaks for each contrast.

8. Peak detection (HOMER)
Peak finding was performed using HOMER. Three detection types were performed: Peaks, Regions, and SuperEnhancers. Please see the HOMER documentation for details. The following table provides links to the bedGraph files for each detection type in each condition, and to an Excel file containing the results of each detection type split by genomic region (e.g. Promoters, Exons, Introns, Intergenic). The Combined file contains the results of each detection type in all conditions (one sheet per condition).

ConditionCountbedGraphClassified
Peaks
NTKO-EZM-K27ac6,531NTKO-EZM-K27ac.tags.d/peaks.txtNTKO-EZM-K27ac-peaks-distr.xlsx
NTKO-EZM-K27me34NTKO-EZM-K27me3.tags.d/peaks.txtNTKO-EZM-K27me3-peaks-distr.xlsx
NTKO-EZM-K36me2568NTKO-EZM-K36me2.tags.d/peaks.txtNTKO-EZM-K36me2-peaks-distr.xlsx
NTKO-EZM-K36me321NTKO-EZM-K36me3.tags.d/peaks.txtNTKO-EZM-K36me3-peaks-distr.xlsx
NTKO-EZM-K4me1628NTKO-EZM-K4me1.tags.d/peaks.txtNTKO-EZM-K4me1-peaks-distr.xlsx
NTKO-EZM-K4me31,812NTKO-EZM-K4me3.tags.d/peaks.txtNTKO-EZM-K4me3-peaks-distr.xlsx
NTKO-ctl-K27ac4,570NTKO-ctl-K27ac.tags.d/peaks.txtNTKO-ctl-K27ac-peaks-distr.xlsx
NTKO-ctl-K27me33,430NTKO-ctl-K27me3.tags.d/peaks.txtNTKO-ctl-K27me3-peaks-distr.xlsx
NTKO-ctl-K36me23,592NTKO-ctl-K36me2.tags.d/peaks.txtNTKO-ctl-K36me2-peaks-distr.xlsx
NTKO-ctl-K36me32,651NTKO-ctl-K36me3.tags.d/peaks.txtNTKO-ctl-K36me3-peaks-distr.xlsx
NTKO-ctl-K4me10NTKO-ctl-K4me1.tags.d/peaks.txtNTKO-ctl-K4me1-peaks-distr.xlsx
NTKO-ctl-K4me3111NTKO-ctl-K4me3.tags.d/peaks.txtNTKO-ctl-K4me3-peaks-distr.xlsx
TKO-EZM-K27ac1,148TKO-EZM-K27ac.tags.d/peaks.txtTKO-EZM-K27ac-peaks-distr.xlsx
TKO-EZM-K27me34,926TKO-EZM-K27me3.tags.d/peaks.txtTKO-EZM-K27me3-peaks-distr.xlsx
TKO-EZM-K36me216,976TKO-EZM-K36me2.tags.d/peaks.txtTKO-EZM-K36me2-peaks-distr.xlsx
TKO-EZM-K36me318TKO-EZM-K36me3.tags.d/peaks.txtTKO-EZM-K36me3-peaks-distr.xlsx
TKO-EZM-K4me115TKO-EZM-K4me1.tags.d/peaks.txtTKO-EZM-K4me1-peaks-distr.xlsx
TKO-EZM-K4me34,420TKO-EZM-K4me3.tags.d/peaks.txtTKO-EZM-K4me3-peaks-distr.xlsx
TKO-ctl-K27ac1,303TKO-ctl-K27ac.tags.d/peaks.txtTKO-ctl-K27ac-peaks-distr.xlsx
TKO-ctl-K27me34,502TKO-ctl-K27me3.tags.d/peaks.txtTKO-ctl-K27me3-peaks-distr.xlsx
TKO-ctl-K36me227,195TKO-ctl-K36me2.tags.d/peaks.txtTKO-ctl-K36me2-peaks-distr.xlsx
TKO-ctl-K36me33,211TKO-ctl-K36me3.tags.d/peaks.txtTKO-ctl-K36me3-peaks-distr.xlsx
TKO-ctl-K4me113,242TKO-ctl-K4me1.tags.d/peaks.txtTKO-ctl-K4me1-peaks-distr.xlsx
TKO-ctl-K4me33,166TKO-ctl-K4me3.tags.d/peaks.txtTKO-ctl-K4me3-peaks-distr.xlsx
Combined104,040peaks.xlsx 
Regions
NTKO-EZM-K27ac8,713NTKO-EZM-K27ac.tags.d/regions.txtNTKO-EZM-K27ac-regions-distr.xlsx
NTKO-EZM-K27me37NTKO-EZM-K27me3.tags.d/regions.txtNTKO-EZM-K27me3-regions-distr.xlsx
NTKO-EZM-K36me21,671NTKO-EZM-K36me2.tags.d/regions.txtNTKO-EZM-K36me2-regions-distr.xlsx
NTKO-EZM-K36me3400NTKO-EZM-K36me3.tags.d/regions.txtNTKO-EZM-K36me3-regions-distr.xlsx
NTKO-EZM-K4me12,821NTKO-EZM-K4me1.tags.d/regions.txtNTKO-EZM-K4me1-regions-distr.xlsx
NTKO-EZM-K4me32,574NTKO-EZM-K4me3.tags.d/regions.txtNTKO-EZM-K4me3-regions-distr.xlsx
NTKO-ctl-K27ac9,314NTKO-ctl-K27ac.tags.d/regions.txtNTKO-ctl-K27ac-regions-distr.xlsx
NTKO-ctl-K27me34,753NTKO-ctl-K27me3.tags.d/regions.txtNTKO-ctl-K27me3-regions-distr.xlsx
NTKO-ctl-K36me210,941NTKO-ctl-K36me2.tags.d/regions.txtNTKO-ctl-K36me2-regions-distr.xlsx
NTKO-ctl-K36me36,494NTKO-ctl-K36me3.tags.d/regions.txtNTKO-ctl-K36me3-regions-distr.xlsx
NTKO-ctl-K4me12NTKO-ctl-K4me1.tags.d/regions.txtNTKO-ctl-K4me1-regions-distr.xlsx
NTKO-ctl-K4me3119NTKO-ctl-K4me3.tags.d/regions.txtNTKO-ctl-K4me3-regions-distr.xlsx
TKO-EZM-K27ac3,425TKO-EZM-K27ac.tags.d/regions.txtTKO-EZM-K27ac-regions-distr.xlsx
TKO-EZM-K27me311,528TKO-EZM-K27me3.tags.d/regions.txtTKO-EZM-K27me3-regions-distr.xlsx
TKO-EZM-K36me224,692TKO-EZM-K36me2.tags.d/regions.txtTKO-EZM-K36me2-regions-distr.xlsx
TKO-EZM-K36me359TKO-EZM-K36me3.tags.d/regions.txtTKO-EZM-K36me3-regions-distr.xlsx
TKO-EZM-K4me118TKO-EZM-K4me1.tags.d/regions.txtTKO-EZM-K4me1-regions-distr.xlsx
TKO-EZM-K4me35,307TKO-EZM-K4me3.tags.d/regions.txtTKO-EZM-K4me3-regions-distr.xlsx
TKO-ctl-K27ac2,827TKO-ctl-K27ac.tags.d/regions.txtTKO-ctl-K27ac-regions-distr.xlsx
TKO-ctl-K27me38,014TKO-ctl-K27me3.tags.d/regions.txtTKO-ctl-K27me3-regions-distr.xlsx
TKO-ctl-K36me235,731TKO-ctl-K36me2.tags.d/regions.txtTKO-ctl-K36me2-regions-distr.xlsx
TKO-ctl-K36me38,563TKO-ctl-K36me3.tags.d/regions.txtTKO-ctl-K36me3-regions-distr.xlsx
TKO-ctl-K4me122,706TKO-ctl-K4me1.tags.d/regions.txtTKO-ctl-K4me1-regions-distr.xlsx
TKO-ctl-K4me34,537TKO-ctl-K4me3.tags.d/regions.txtTKO-ctl-K4me3-regions-distr.xlsx
Combined175,216regions.xlsx 
Enhancers
NTKO-EZM-K27ac154NTKO-EZM-K27ac.tags.d/superEnhancers.txtNTKO-EZM-K27ac-enhancers-distr.xlsx
NTKO-EZM-K27me33NTKO-EZM-K27me3.tags.d/superEnhancers.txtNTKO-EZM-K27me3-enhancers-distr.xlsx
NTKO-EZM-K36me233NTKO-EZM-K36me2.tags.d/superEnhancers.txtNTKO-EZM-K36me2-enhancers-distr.xlsx
NTKO-EZM-K36me36NTKO-EZM-K36me3.tags.d/superEnhancers.txtNTKO-EZM-K36me3-enhancers-distr.xlsx
NTKO-EZM-K4me120NTKO-EZM-K4me1.tags.d/superEnhancers.txtNTKO-EZM-K4me1-enhancers-distr.xlsx
NTKO-EZM-K4me365NTKO-EZM-K4me3.tags.d/superEnhancers.txtNTKO-EZM-K4me3-enhancers-distr.xlsx
NTKO-ctl-K27ac90NTKO-ctl-K27ac.tags.d/superEnhancers.txtNTKO-ctl-K27ac-enhancers-distr.xlsx
NTKO-ctl-K27me326NTKO-ctl-K27me3.tags.d/superEnhancers.txtNTKO-ctl-K27me3-enhancers-distr.xlsx
NTKO-ctl-K36me228NTKO-ctl-K36me2.tags.d/superEnhancers.txtNTKO-ctl-K36me2-enhancers-distr.xlsx
NTKO-ctl-K36me317NTKO-ctl-K36me3.tags.d/superEnhancers.txtNTKO-ctl-K36me3-enhancers-distr.xlsx
NTKO-ctl-K4me10NTKO-ctl-K4me1.tags.d/superEnhancers.txtNTKO-ctl-K4me1-enhancers-distr.xlsx
NTKO-ctl-K4me39NTKO-ctl-K4me3.tags.d/superEnhancers.txtNTKO-ctl-K4me3-enhancers-distr.xlsx
TKO-EZM-K27ac36TKO-EZM-K27ac.tags.d/superEnhancers.txtTKO-EZM-K27ac-enhancers-distr.xlsx
TKO-EZM-K27me361TKO-EZM-K27me3.tags.d/superEnhancers.txtTKO-EZM-K27me3-enhancers-distr.xlsx
TKO-EZM-K36me2282TKO-EZM-K36me2.tags.d/superEnhancers.txtTKO-EZM-K36me2-enhancers-distr.xlsx
TKO-EZM-K36me36TKO-EZM-K36me3.tags.d/superEnhancers.txtTKO-EZM-K36me3-enhancers-distr.xlsx
TKO-EZM-K4me16TKO-EZM-K4me1.tags.d/superEnhancers.txtTKO-EZM-K4me1-enhancers-distr.xlsx
TKO-EZM-K4me379TKO-EZM-K4me3.tags.d/superEnhancers.txtTKO-EZM-K4me3-enhancers-distr.xlsx
TKO-ctl-K27ac62TKO-ctl-K27ac.tags.d/superEnhancers.txtTKO-ctl-K27ac-enhancers-distr.xlsx
TKO-ctl-K27me338TKO-ctl-K27me3.tags.d/superEnhancers.txtTKO-ctl-K27me3-enhancers-distr.xlsx
TKO-ctl-K36me2470TKO-ctl-K36me2.tags.d/superEnhancers.txtTKO-ctl-K36me2-enhancers-distr.xlsx
TKO-ctl-K36me318TKO-ctl-K36me3.tags.d/superEnhancers.txtTKO-ctl-K36me3-enhancers-distr.xlsx
TKO-ctl-K4me1296TKO-ctl-K4me1.tags.d/superEnhancers.txtTKO-ctl-K4me1-enhancers-distr.xlsx
TKO-ctl-K4me3109TKO-ctl-K4me3.tags.d/superEnhancers.txtTKO-ctl-K4me3-enhancers-distr.xlsx
Combined1,914enhancers.xlsx 
Table 14. Results of peak detection with HOMER.

The following plots show the distribution of peak locations in the different conditions.
9. Differential peak finding
Differential peak finding was performed using the HOMER getDifferentialPeaks command. The following files contain the peaks showing significant differences in each contrast.

TestControlTest peaksControl peaksDiffPeaks
NTKO-EZM-K27acNTKO-ctl-K27ac46123476NTKO-EZM-K27ac.vs.NTKO-ctl-K27ac.diffPeaks.xlsx
TKO-EZM-K27acTKO-ctl-K27ac832701TKO-EZM-K27ac.vs.TKO-ctl-K27ac.diffPeaks.xlsx
TKO-ctl-K27acNTKO-ctl-K27ac11874380TKO-ctl-K27ac.vs.NTKO-ctl-K27ac.diffPeaks.xlsx
NTKO-EZM-K27me3NTKO-ctl-K27me313429NTKO-EZM-K27me3.vs.NTKO-ctl-K27me3.diffPeaks.xlsx
TKO-EZM-K27me3TKO-ctl-K27me338673713TKO-EZM-K27me3.vs.TKO-ctl-K27me3.diffPeaks.xlsx
TKO-ctl-K27me3NTKO-ctl-K27me339632953TKO-ctl-K27me3.vs.NTKO-ctl-K27me3.diffPeaks.xlsx
NTKO-EZM-K36me3NTKO-ctl-K36me3181635NTKO-EZM-K36me3.vs.NTKO-ctl-K36me3.diffPeaks.xlsx
TKO-EZM-K36me3TKO-ctl-K36me313211TKO-EZM-K36me3.vs.TKO-ctl-K36me3.diffPeaks.xlsx
TKO-ctl-K36me3NTKO-ctl-K36me325091891TKO-ctl-K36me3.vs.NTKO-ctl-K36me3.diffPeaks.xlsx
NTKO-EZM-K4me1NTKO-ctl-K4me100NTKO-EZM-K4me1.vs.NTKO-ctl-K4me1.diffPeaks.xlsx
TKO-EZM-K4me1TKO-ctl-K4me1213241TKO-EZM-K4me1.vs.TKO-ctl-K4me1.diffPeaks.xlsx
TKO-ctl-K4me1NTKO-ctl-K4me100TKO-ctl-K4me1.vs.NTKO-ctl-K4me1.diffPeaks.xlsx
NTKO-EZM-K4me3NTKO-ctl-K4me31580111NTKO-EZM-K4me3.vs.NTKO-ctl-K4me3.diffPeaks.xlsx
TKO-EZM-K4me3TKO-ctl-K4me336562485TKO-EZM-K4me3.vs.TKO-ctl-K4me3.diffPeaks.xlsx
TKO-ctl-K4me3NTKO-ctl-K4me3964111TKO-ctl-K4me3.vs.NTKO-ctl-K4me3.diffPeaks.xlsx
NTKO-EZM-K36me2NTKO-ctl-K36me24752990NTKO-EZM-K36me2.vs.NTKO-ctl-K36me2.diffPeaks.xlsx
TKO-EZM-K36me2TKO-ctl-K36me21593325602TKO-EZM-K36me2.vs.TKO-ctl-K36me2.diffPeaks.xlsx
TKO-ctl-K36me2NTKO-ctl-K36me2263143582TKO-ctl-K36me2.vs.NTKO-ctl-K36me2.diffPeaks.xlsx
Table 15. Results of differential peak detection with HOMER.

10. Motif finding
ChIP-Seq peaks were analyzed with the HOMER findMotifs function. The links in the following table lead to the motif finding report for each condition.

ConditionKnownde novo
NTKO-EZM-K27acNTKO-EZM-K27ac.motifs/knownResults.htmlNTKO-EZM-K27ac.motifs/homerResults.html
NTKO-EZM-K27me3NTKO-EZM-K27me3.motifs/knownResults.htmlNTKO-EZM-K27me3.motifs/homerResults.html
NTKO-EZM-K36me2NTKO-EZM-K36me2.motifs/knownResults.htmlNTKO-EZM-K36me2.motifs/homerResults.html
NTKO-EZM-K36me3NTKO-EZM-K36me3.motifs/knownResults.htmlNTKO-EZM-K36me3.motifs/homerResults.html
NTKO-EZM-K4me1NTKO-EZM-K4me1.motifs/knownResults.htmlNTKO-EZM-K4me1.motifs/homerResults.html
NTKO-EZM-K4me3NTKO-EZM-K4me3.motifs/knownResults.htmlNTKO-EZM-K4me3.motifs/homerResults.html
NTKO-ctl-K27acNTKO-ctl-K27ac.motifs/knownResults.htmlNTKO-ctl-K27ac.motifs/homerResults.html
NTKO-ctl-K27me3NTKO-ctl-K27me3.motifs/knownResults.htmlNTKO-ctl-K27me3.motifs/homerResults.html
NTKO-ctl-K36me2NTKO-ctl-K36me2.motifs/knownResults.htmlNTKO-ctl-K36me2.motifs/homerResults.html
NTKO-ctl-K36me3NTKO-ctl-K36me3.motifs/knownResults.htmlNTKO-ctl-K36me3.motifs/homerResults.html
NTKO-ctl-K4me1NTKO-ctl-K4me1.motifs/knownResults.htmlNTKO-ctl-K4me1.motifs/homerResults.html
NTKO-ctl-K4me3NTKO-ctl-K4me3.motifs/knownResults.htmlNTKO-ctl-K4me3.motifs/homerResults.html
TKO-EZM-K27acTKO-EZM-K27ac.motifs/knownResults.htmlTKO-EZM-K27ac.motifs/homerResults.html
TKO-EZM-K27me3TKO-EZM-K27me3.motifs/knownResults.htmlTKO-EZM-K27me3.motifs/homerResults.html
TKO-EZM-K36me2TKO-EZM-K36me2.motifs/knownResults.htmlTKO-EZM-K36me2.motifs/homerResults.html
TKO-EZM-K36me3TKO-EZM-K36me3.motifs/knownResults.htmlTKO-EZM-K36me3.motifs/homerResults.html
TKO-EZM-K4me1TKO-EZM-K4me1.motifs/knownResults.htmlTKO-EZM-K4me1.motifs/homerResults.html
TKO-EZM-K4me3TKO-EZM-K4me3.motifs/knownResults.htmlTKO-EZM-K4me3.motifs/homerResults.html
TKO-ctl-K27acTKO-ctl-K27ac.motifs/knownResults.htmlTKO-ctl-K27ac.motifs/homerResults.html
TKO-ctl-K27me3TKO-ctl-K27me3.motifs/knownResults.htmlTKO-ctl-K27me3.motifs/homerResults.html
TKO-ctl-K36me2TKO-ctl-K36me2.motifs/knownResults.htmlTKO-ctl-K36me2.motifs/homerResults.html
TKO-ctl-K36me3TKO-ctl-K36me3.motifs/knownResults.htmlTKO-ctl-K36me3.motifs/homerResults.html
TKO-ctl-K4me1TKO-ctl-K4me1.motifs/knownResults.htmlTKO-ctl-K4me1.motifs/homerResults.html
TKO-ctl-K4me3TKO-ctl-K4me3.motifs/knownResults.htmlTKO-ctl-K4me3.motifs/homerResults.html
Table 16. Results of motif finding with HOMER.

11. MultiQC report
MultiQC is a general Quality Control tool for a large number of bioinformatics pipelines. The report on this analysis (generated using MultiQC version 1.12) is available here:

MultiQC report
12. UCSC hub

UCSC Genome Browser: use the previous link to display the data tracks automatically, or copy the the URL http://licht:licht@lichtlab.cancer.ufl.edu/reports/UTX//NS3143/NS3143/hub.txt and paste it into the "My Hubs" form in this page.

WashU EpiGenome Browser: use the previous link to display the data tracks automatically, or copy the following URL into the "Datahub by URL Link" field: http://licht:licht@lichtlab.cancer.ufl.edu/reports/UTX//NS3143/NS3143/hub.json.



Completed: 9-15-2023@16:37
© 2023, A. Riva, University of Florida.