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Cut&Run - Alignment and peak finding

Title: NS3570
Project: (none)
Started on: 1/9/2024 5:36:43
Hostname: login7.ufhpc
Run directory: /blue/licht/runs/Evans-MDS/NS3570/NS3570
Configuration NS3570.conf
Table of contents:
  1. Input data
  2. Trimming and quality control
  3. Mapping to genome
  4. Spike-ins normalization
  5. Genome coverage
  6. Peak detection
  7. Fraction of Reads in Peaks
  8. Differential peak detection
  9. MultiQC report
  10. 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
Reference genome:hg38
Experimental conditions:Beas2B-Parental-aH3, Beas2B-Parental-aH3K4me3, Beas2B-Parental-aHA, Beas2B-H3WT-HA-aH3, Beas2B-H3WT-HA-aH3K4me3, Beas2B-H3WT-HA-aHA, Beas2B-H3E97K-HA-Clone19-aH3, Beas2B-H3E97K-HA-Clone19-aH3K4me3, Beas2B-H3E97K-HA-Clone19-aHA, Beas2B-H3E97K-HA-Clone22-aH3, Beas2B-H3E97K-HA-Clone22-aH3K4me3, Beas2B-H3E97K-HA-Clone22-aHA, Beas2B-H3E97K-HA-Clone23-aH3, Beas2B-H3E97K-HA-Clone23-aH3K4me3, Beas2B-H3E97K-HA-Clone23-aHA
Contrasts:Beas2B-H3WT-HA-aH3 vs. Beas2B-Parental-aH3, Beas2B-H3E97K-HA-Clone19-aH3 vs. Beas2B-Parental-aH3, Beas2B-H3E97K-HA-Clone22-aH3 vs. Beas2B-Parental-aH3, Beas2B-H3E97K-HA-Clone23-aH3 vs. Beas2B-Parental-aH3, Beas2B-H3WT-HA-aH3K4me3 vs. Beas2B-Parental-aH3K4me3, Beas2B-H3E97K-HA-Clone19-aH3K4me3 vs. Beas2B-Parental-aH3K4me3, Beas2B-H3E97K-HA-Clone22-aH3K4me3 vs. Beas2B-Parental-aH3K4me3, Beas2B-H3E97K-HA-Clone23-aH3K4me3 vs. Beas2B-Parental-aH3K4me3, Beas2B-H3WT-HA-aHA vs. Beas2B-Parental-aHA, Beas2B-H3E97K-HA-Clone19-aHA vs. Beas2B-Parental-aHA, Beas2B-H3E97K-HA-Clone22-aHA vs. Beas2B-Parental-aHA, Beas2B-H3E97K-HA-Clone23-aHA vs. Beas2B-Parental-aHA, Beas2B-H3E97K-HA-Clone19-aHA vs. Beas2B-H3WT-HA-aHA, Beas2B-H3E97K-HA-Clone22-aHA vs. Beas2B-H3WT-HA-aHA, Beas2B-H3E97K-HA-Clone23-aHA vs. Beas2B-H3WT-HA-aHA, Beas2B-H3E97K-HA-Clone19-aH3 vs. Beas2B-H3WT-HA-aH3, Beas2B-H3E97K-HA-Clone22-aH3 vs. Beas2B-H3WT-HA-aH3, Beas2B-H3E97K-HA-Clone23-aH3 vs. Beas2B-H3WT-HA-aH3, Beas2B-H3E97K-HA-Clone19-aH3K4me3 vs. Beas2B-H3WT-HA-aH3K4me3, Beas2B-H3E97K-HA-Clone22-aH3K4me3 vs. Beas2B-H3WT-HA-aH3K4me3, Beas2B-H3E97K-HA-Clone23-aH3K4me3 vs. Beas2B-H3WT-HA-aH3K4me3
Number of samples40
Sequencing data data
Total number of reads:1,230,360,200
Average reads per sample:30,759,005
Table 1. Summary of input data



ConditionSampleNumber of reads% Reads
Beas2B-Parental-aH3Beas2B-Parental-aH3-127,270,5242.22%
Beas2B-Parental-aH3-235,709,0012.90%
Beas2B-Parental-aH3K4me3Beas2B-Parental-aH3K4me3-131,844,6092.59%
Beas2B-Parental-aH3K4me3-229,145,7542.37%
Beas2B-Parental-aHABeas2B-Parental-aHA-130,090,3332.45%
Beas2B-Parental-aHA-229,573,8102.40%
Beas2B-H3WT-HA-aH3Beas2B-H3WT-HA-aH3-130,300,1452.46%
Beas2B-H3WT-HA-aH3-234,536,7292.81%
Beas2B-H3WT-HA-aH3K4me3Beas2B-H3WT-HA-aH3K4me3-138,235,9523.11%
Beas2B-H3WT-HA-aH3K4me3-236,649,2762.98%
Beas2B-H3WT-HA-aHABeas2B-H3WT-HA-aHA-136,560,4882.97%
Beas2B-H3WT-HA-aHA-240,144,1783.26%
Beas2B-H3E97K-HA-Clone19-aH3Beas2B-H3E97K-HA-Clone19-aH3-140,831,4923.32%
Beas2B-H3E97K-HA-Clone19-aH3-239,806,7423.24%
Beas2B-H3E97K-HA-Clone19-aH3K4me3Beas2B-H3E97K-HA-Clone19-aH3K4me3-123,892,4921.94%
Beas2B-H3E97K-HA-Clone19-aH3K4me3-227,196,3642.21%
Beas2B-H3E97K-HA-Clone19-aHABeas2B-H3E97K-HA-Clone19-aHA-125,397,9272.06%
Beas2B-H3E97K-HA-Clone19-aHA-220,383,7421.66%
Beas2B-H3E97K-HA-Clone22-aH3Beas2B-H3E97K-HA-Clone22-aH3-127,067,7682.20%
Beas2B-H3E97K-HA-Clone22-aH3-229,416,5882.39%
Beas2B-H3E97K-HA-Clone22-aH3K4me3Beas2B-H3E97K-HA-Clone22-aH3K4me3-130,839,1262.51%
Beas2B-H3E97K-HA-Clone22-aH3K4me3-230,509,6842.48%
Beas2B-H3E97K-HA-Clone22-aHABeas2B-H3E97K-HA-Clone22-aHA-136,608,0342.98%
Beas2B-H3E97K-HA-Clone22-aHA-232,732,6182.66%
Beas2B-H3E97K-HA-Clone23-aH3Beas2B-H3E97K-HA-Clone23-aH3-120,421,8241.66%
Beas2B-H3E97K-HA-Clone23-aH3-219,850,1251.61%
Beas2B-H3E97K-HA-Clone23-aH3K4me3Beas2B-H3E97K-HA-Clone23-aH3K4me3-129,340,7422.38%
Beas2B-H3E97K-HA-Clone23-aH3K4me3-230,080,4482.44%
Beas2B-H3E97K-HA-Clone23-aHABeas2B-H3E97K-HA-Clone23-aHA-133,986,2442.76%
Beas2B-H3E97K-HA-Clone23-aHA-229,423,8542.39%
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
Beas2B-Parental-aH3-1Beas2B-Parental-aH3-1_r127,270,524Beas2B-H3WT-HA-aH3-1_S15_L008_R1_001
Beas2B-H3WT-HA-aH3-1_S15_L008_R2_001		26,719,189Beas2B-H3WT-HA-aH3-1_S15_L008_R1_001.trim.paired
Beas2B-H3WT-HA-aH3-1_S15_L008_R2_001.trim.paired		97.98%
Beas2B-Parental-aH3-2Beas2B-Parental-aH3-2_r135,709,001Beas2B-H3WT-HA-aH3-2_S16_L008_R1_001
Beas2B-H3WT-HA-aH3-2_S16_L008_R2_001		35,080,086Beas2B-H3WT-HA-aH3-2_S16_L008_R1_001.trim.paired
Beas2B-H3WT-HA-aH3-2_S16_L008_R2_001.trim.paired		98.24%
Beas2B-Parental-aIgG-1Beas2B-Parental-aIgG-1_r132,557,968Beas2B-H3WT-HA-aIgG-1_S9_L008_R1_001
Beas2B-H3WT-HA-aIgG-1_S9_L008_R2_001		31,816,193Beas2B-H3WT-HA-aIgG-1_S9_L008_R1_001.trim.paired
Beas2B-H3WT-HA-aIgG-1_S9_L008_R2_001.trim.paired		97.72%
Beas2B-Parental-aIgG-2Beas2B-Parental-aIgG-2_r136,599,747Beas2B-H3WT-HA-aIgG-2_S10_L008_R1_001
Beas2B-H3WT-HA-aIgG-2_S10_L008_R2_001		35,822,597Beas2B-H3WT-HA-aIgG-2_S10_L008_R1_001.trim.paired
Beas2B-H3WT-HA-aIgG-2_S10_L008_R2_001.trim.paired		97.88%
Beas2B-Parental-aH3K4me3-1Beas2B-Parental-aH3K4me3-1_r131,844,609Beas2B-H3WT-HA-aH3K4me3-1_S11_L008_R1_001
Beas2B-H3WT-HA-aH3K4me3-1_S11_L008_R2_001		31,245,224Beas2B-H3WT-HA-aH3K4me3-1_S11_L008_R1_001.trim.paired
Beas2B-H3WT-HA-aH3K4me3-1_S11_L008_R2_001.trim.paired		98.12%
Beas2B-Parental-aH3K4me3-2Beas2B-Parental-aH3K4me3-2_r129,145,754Beas2B-H3WT-HA-aH3K4me3-2_S12_L008_R1_001
Beas2B-H3WT-HA-aH3K4me3-2_S12_L008_R2_001		28,620,850Beas2B-H3WT-HA-aH3K4me3-2_S12_L008_R1_001.trim.paired
Beas2B-H3WT-HA-aH3K4me3-2_S12_L008_R2_001.trim.paired		98.20%
Beas2B-Parental-aHA-1Beas2B-Parental-aHA-1_r130,090,333Beas2B-H3WT-HA-aHA-1_S13_L008_R1_001
Beas2B-H3WT-HA-aHA-1_S13_L008_R2_001		29,493,766Beas2B-H3WT-HA-aHA-1_S13_L008_R1_001.trim.paired
Beas2B-H3WT-HA-aHA-1_S13_L008_R2_001.trim.paired		98.02%
Beas2B-Parental-aHA-2Beas2B-Parental-aHA-2_r129,573,810Beas2B-H3WT-HA-aHA-2_S14_L008_R1_001
Beas2B-H3WT-HA-aHA-2_S14_L008_R2_001		29,026,743Beas2B-H3WT-HA-aHA-2_S14_L008_R1_001.trim.paired
Beas2B-H3WT-HA-aHA-2_S14_L008_R2_001.trim.paired		98.15%
Beas2B-H3WT-HA-aH3-1Beas2B-H3WT-HA-aH3-1_r130,300,145Beas2B-Parental-aH3-1_S7_L008_R1_001
Beas2B-Parental-aH3-1_S7_L008_R2_001		29,573,357Beas2B-Parental-aH3-1_S7_L008_R1_001.trim.paired
Beas2B-Parental-aH3-1_S7_L008_R2_001.trim.paired		97.60%
Beas2B-H3WT-HA-aH3-2Beas2B-H3WT-HA-aH3-2_r134,536,729Beas2B-Parental-aH3-2_S8_L008_R1_001
Beas2B-Parental-aH3-2_S8_L008_R2_001		33,720,406Beas2B-Parental-aH3-2_S8_L008_R1_001.trim.paired
Beas2B-Parental-aH3-2_S8_L008_R2_001.trim.paired		97.64%
Beas2B-H3WT-HA-aIgG-1Beas2B-H3WT-HA-aIgG-1_r137,079,340Beas2B-Parental-aIgG-1_S1_L008_R1_001
Beas2B-Parental-aIgG-1_S1_L008_R2_001		36,473,761Beas2B-Parental-aIgG-1_S1_L008_R1_001.trim.paired
Beas2B-Parental-aIgG-1_S1_L008_R2_001.trim.paired		98.37%
Beas2B-H3WT-HA-aIgG-2Beas2B-H3WT-HA-aIgG-2_r135,354,696Beas2B-Parental-aIgG-2_S2_L008_R1_001
Beas2B-Parental-aIgG-2_S2_L008_R2_001		34,667,075Beas2B-Parental-aIgG-2_S2_L008_R1_001.trim.paired
Beas2B-Parental-aIgG-2_S2_L008_R2_001.trim.paired		98.06%
Beas2B-H3WT-HA-aH3K4me3-1Beas2B-H3WT-HA-aH3K4me3-1_r138,235,952Beas2B-Parental-aH3K4me3-1_S3_L008_R1_001
Beas2B-Parental-aH3K4me3-1_S3_L008_R2_001		37,473,027Beas2B-Parental-aH3K4me3-1_S3_L008_R1_001.trim.paired
Beas2B-Parental-aH3K4me3-1_S3_L008_R2_001.trim.paired		98.00%
Beas2B-H3WT-HA-aH3K4me3-2Beas2B-H3WT-HA-aH3K4me3-2_r136,649,276Beas2B-Parental-aH3K4me3-2_S4_L008_R1_001
Beas2B-Parental-aH3K4me3-2_S4_L008_R2_001		35,903,365Beas2B-Parental-aH3K4me3-2_S4_L008_R1_001.trim.paired
Beas2B-Parental-aH3K4me3-2_S4_L008_R2_001.trim.paired		97.96%
Beas2B-H3WT-HA-aHA-1Beas2B-H3WT-HA-aHA-1_r136,560,488Beas2B-Parental-aHA-1_S5_L008_R1_001
Beas2B-Parental-aHA-1_S5_L008_R2_001		35,740,498Beas2B-Parental-aHA-1_S5_L008_R1_001.trim.paired
Beas2B-Parental-aHA-1_S5_L008_R2_001.trim.paired		97.76%
Beas2B-H3WT-HA-aHA-2Beas2B-H3WT-HA-aHA-2_r140,144,178Beas2B-Parental-aHA-2_S6_L008_R1_001
Beas2B-Parental-aHA-2_S6_L008_R2_001		39,243,650Beas2B-Parental-aHA-2_S6_L008_R1_001.trim.paired
Beas2B-Parental-aHA-2_S6_L008_R2_001.trim.paired		97.76%
Beas2B-H3E97K-HA-Clone19-aH3-1Beas2B-H3E97K-HA-Clone19-aH3-1_r140,831,492Beas2B-H3E97K-HA-Clone19-aH3-1_S23_L008_R1_001
Beas2B-H3E97K-HA-Clone19-aH3-1_S23_L008_R2_001		40,118,114Beas2B-H3E97K-HA-Clone19-aH3-1_S23_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone19-aH3-1_S23_L008_R2_001.trim.paired		98.25%
Beas2B-H3E97K-HA-Clone19-aH3-2Beas2B-H3E97K-HA-Clone19-aH3-2_r139,806,742Beas2B-H3E97K-HA-Clone19-aH3-2_S24_L008_R1_001
Beas2B-H3E97K-HA-Clone19-aH3-2_S24_L008_R2_001		39,079,956Beas2B-H3E97K-HA-Clone19-aH3-2_S24_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone19-aH3-2_S24_L008_R2_001.trim.paired		98.17%
Beas2B-H3E97K-HA-Clone19-aIgG-1Beas2B-H3E97K-HA-Clone19-aIgG-1_r122,505,256Beas2B-H3E97K-HA-Clone19-aIgG-1_S17_L008_R1_001
Beas2B-H3E97K-HA-Clone19-aIgG-1_S17_L008_R2_001		22,114,478Beas2B-H3E97K-HA-Clone19-aIgG-1_S17_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone19-aIgG-1_S17_L008_R2_001.trim.paired		98.26%
Beas2B-H3E97K-HA-Clone19-aIgG-2Beas2B-H3E97K-HA-Clone19-aIgG-2_r121,527,845Beas2B-H3E97K-HA-Clone19-aIgG-2_S18_L008_R1_001
Beas2B-H3E97K-HA-Clone19-aIgG-2_S18_L008_R2_001		21,155,392Beas2B-H3E97K-HA-Clone19-aIgG-2_S18_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone19-aIgG-2_S18_L008_R2_001.trim.paired		98.27%
Beas2B-H3E97K-HA-Clone19-aH3K4me3-1Beas2B-H3E97K-HA-Clone19-aH3K4me3-1_r123,892,492Beas2B-H3E97K-HA-Clone19-aH3K4me3-1_S19_L008_R1_001
Beas2B-H3E97K-HA-Clone19-aH3K4me3-1_S19_L008_R2_001		23,378,916Beas2B-H3E97K-HA-Clone19-aH3K4me3-1_S19_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone19-aH3K4me3-1_S19_L008_R2_001.trim.paired		97.85%
Beas2B-H3E97K-HA-Clone19-aH3K4me3-2Beas2B-H3E97K-HA-Clone19-aH3K4me3-2_r127,196,364Beas2B-H3E97K-HA-Clone19-aH3K4me3-2_S20_L008_R1_001
Beas2B-H3E97K-HA-Clone19-aH3K4me3-2_S20_L008_R2_001		26,606,166Beas2B-H3E97K-HA-Clone19-aH3K4me3-2_S20_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone19-aH3K4me3-2_S20_L008_R2_001.trim.paired		97.83%
Beas2B-H3E97K-HA-Clone19-aHA-1Beas2B-H3E97K-HA-Clone19-aHA-1_r125,397,927Beas2B-H3E97K-HA-Clone19-aHA-1_S21_L008_R1_001
Beas2B-H3E97K-HA-Clone19-aHA-1_S21_L008_R2_001		25,016,445Beas2B-H3E97K-HA-Clone19-aHA-1_S21_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone19-aHA-1_S21_L008_R2_001.trim.paired		98.50%
Beas2B-H3E97K-HA-Clone19-aHA-2Beas2B-H3E97K-HA-Clone19-aHA-2_r120,383,742Beas2B-H3E97K-HA-Clone19-aHA-2_S22_L008_R1_001
Beas2B-H3E97K-HA-Clone19-aHA-2_S22_L008_R2_001		20,040,090Beas2B-H3E97K-HA-Clone19-aHA-2_S22_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone19-aHA-2_S22_L008_R2_001.trim.paired		98.31%
Beas2B-H3E97K-HA-Clone22-aH3-1Beas2B-H3E97K-HA-Clone22-aH3-1_r127,067,768Beas2B-H3E97K-HA-Clone22-aH3-1_S31_L008_R1_001
Beas2B-H3E97K-HA-Clone22-aH3-1_S31_L008_R2_001		26,550,563Beas2B-H3E97K-HA-Clone22-aH3-1_S31_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone22-aH3-1_S31_L008_R2_001.trim.paired		98.09%
Beas2B-H3E97K-HA-Clone22-aH3-2Beas2B-H3E97K-HA-Clone22-aH3-2_r129,416,588Beas2B-H3E97K-HA-Clone22-aH3-2_S32_L008_R1_001
Beas2B-H3E97K-HA-Clone22-aH3-2_S32_L008_R2_001		28,876,697Beas2B-H3E97K-HA-Clone22-aH3-2_S32_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone22-aH3-2_S32_L008_R2_001.trim.paired		98.16%
Beas2B-H3E97K-HA-Clone22-aIgG-1Beas2B-H3E97K-HA-Clone22-aIgG-1_r130,213,440Beas2B-H3E97K-HA-Clone22-aIgG-1_S25_L008_R1_001
Beas2B-H3E97K-HA-Clone22-aIgG-1_S25_L008_R2_001		29,577,003Beas2B-H3E97K-HA-Clone22-aIgG-1_S25_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone22-aIgG-1_S25_L008_R2_001.trim.paired		97.89%
Beas2B-H3E97K-HA-Clone22-aIgG-2Beas2B-H3E97K-HA-Clone22-aIgG-2_r132,936,479Beas2B-H3E97K-HA-Clone22-aIgG-2_S26_L008_R1_001
Beas2B-H3E97K-HA-Clone22-aIgG-2_S26_L008_R2_001		32,235,755Beas2B-H3E97K-HA-Clone22-aIgG-2_S26_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone22-aIgG-2_S26_L008_R2_001.trim.paired		97.87%
Beas2B-H3E97K-HA-Clone22-aH3K4me3-1Beas2B-H3E97K-HA-Clone22-aH3K4me3-1_r130,839,126Beas2B-H3E97K-HA-Clone22-aH3K4me3-1_S27_L008_R1_001
Beas2B-H3E97K-HA-Clone22-aH3K4me3-1_S27_L008_R2_001		30,340,767Beas2B-H3E97K-HA-Clone22-aH3K4me3-1_S27_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone22-aH3K4me3-1_S27_L008_R2_001.trim.paired		98.38%
Beas2B-H3E97K-HA-Clone22-aH3K4me3-2Beas2B-H3E97K-HA-Clone22-aH3K4me3-2_r130,509,684Beas2B-H3E97K-HA-Clone22-aH3K4me3-2_S28_L008_R1_001
Beas2B-H3E97K-HA-Clone22-aH3K4me3-2_S28_L008_R2_001		29,964,895Beas2B-H3E97K-HA-Clone22-aH3K4me3-2_S28_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone22-aH3K4me3-2_S28_L008_R2_001.trim.paired		98.21%
Beas2B-H3E97K-HA-Clone22-aHA-1Beas2B-H3E97K-HA-Clone22-aHA-1_r136,608,034Beas2B-H3E97K-HA-Clone22-aHA-1_S29_L008_R1_001
Beas2B-H3E97K-HA-Clone22-aHA-1_S29_L008_R2_001		35,900,634Beas2B-H3E97K-HA-Clone22-aHA-1_S29_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone22-aHA-1_S29_L008_R2_001.trim.paired		98.07%
Beas2B-H3E97K-HA-Clone22-aHA-2Beas2B-H3E97K-HA-Clone22-aHA-2_r132,732,618Beas2B-H3E97K-HA-Clone22-aHA-2_S30_L008_R1_001
Beas2B-H3E97K-HA-Clone22-aHA-2_S30_L008_R2_001		32,118,681Beas2B-H3E97K-HA-Clone22-aHA-2_S30_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone22-aHA-2_S30_L008_R2_001.trim.paired		98.12%
Beas2B-H3E97K-HA-Clone23-aH3-1Beas2B-H3E97K-HA-Clone23-aH3-1_r120,421,824Beas2B-H3E97K-HA-Clone23-aH3-1_S39_L008_R1_001
Beas2B-H3E97K-HA-Clone23-aH3-1_S39_L008_R2_001		20,056,127Beas2B-H3E97K-HA-Clone23-aH3-1_S39_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone23-aH3-1_S39_L008_R2_001.trim.paired		98.21%
Beas2B-H3E97K-HA-Clone23-aH3-2Beas2B-H3E97K-HA-Clone23-aH3-2_r119,850,125Beas2B-H3E97K-HA-Clone23-aH3-2_S40_L008_R1_001
Beas2B-H3E97K-HA-Clone23-aH3-2_S40_L008_R2_001		19,516,813Beas2B-H3E97K-HA-Clone23-aH3-2_S40_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone23-aH3-2_S40_L008_R2_001.trim.paired		98.32%
Beas2B-H3E97K-HA-Clone23-aIgG-1Beas2B-H3E97K-HA-Clone23-aIgG-1_r126,922,237Beas2B-H3E97K-HA-Clone23-aIgG-1_S33_L008_R1_001
Beas2B-H3E97K-HA-Clone23-aIgG-1_S33_L008_R2_001		26,379,633Beas2B-H3E97K-HA-Clone23-aIgG-1_S33_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone23-aIgG-1_S33_L008_R2_001.trim.paired		97.98%
Beas2B-H3E97K-HA-Clone23-aIgG-2Beas2B-H3E97K-HA-Clone23-aIgG-2_r126,816,579Beas2B-H3E97K-HA-Clone23-aIgG-2_S34_L008_R1_001
Beas2B-H3E97K-HA-Clone23-aIgG-2_S34_L008_R2_001		26,315,380Beas2B-H3E97K-HA-Clone23-aIgG-2_S34_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone23-aIgG-2_S34_L008_R2_001.trim.paired		98.13%
Beas2B-H3E97K-HA-Clone23-aH3K4me3-1Beas2B-H3E97K-HA-Clone23-aH3K4me3-1_r129,340,742Beas2B-H3E97K-HA-Clone23-aH3K4me3-1_S35_L008_R1_001
Beas2B-H3E97K-HA-Clone23-aH3K4me3-1_S35_L008_R2_001		28,743,556Beas2B-H3E97K-HA-Clone23-aH3K4me3-1_S35_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone23-aH3K4me3-1_S35_L008_R2_001.trim.paired		97.96%
Beas2B-H3E97K-HA-Clone23-aH3K4me3-2Beas2B-H3E97K-HA-Clone23-aH3K4me3-2_r130,080,448Beas2B-H3E97K-HA-Clone23-aH3K4me3-2_S36_L008_R1_001
Beas2B-H3E97K-HA-Clone23-aH3K4me3-2_S36_L008_R2_001		29,455,739Beas2B-H3E97K-HA-Clone23-aH3K4me3-2_S36_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone23-aH3K4me3-2_S36_L008_R2_001.trim.paired		97.92%
Beas2B-H3E97K-HA-Clone23-aHA-1Beas2B-H3E97K-HA-Clone23-aHA-1_r133,986,244Beas2B-H3E97K-HA-Clone23-aHA-1_S37_L008_R1_001
Beas2B-H3E97K-HA-Clone23-aHA-1_S37_L008_R2_001		33,263,033Beas2B-H3E97K-HA-Clone23-aHA-1_S37_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone23-aHA-1_S37_L008_R2_001.trim.paired		97.87%
Beas2B-H3E97K-HA-Clone23-aHA-2Beas2B-H3E97K-HA-Clone23-aHA-2_r129,423,854Beas2B-H3E97K-HA-Clone23-aHA-2_S38_L008_R1_001
Beas2B-H3E97K-HA-Clone23-aHA-2_S38_L008_R2_001		28,866,315Beas2B-H3E97K-HA-Clone23-aHA-2_S38_L008_R1_001.trim.paired
Beas2B-H3E97K-HA-Clone23-aHA-2_S38_L008_R2_001.trim.paired		98.11%
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
Beas2B-Parental-aH3-127,270,52426,719,18997.98%
Beas2B-Parental-aH3-235,709,00135,080,08698.24%
Beas2B-Parental-aIgG-132,557,96831,816,19397.72%
Beas2B-Parental-aIgG-236,599,74735,822,59797.88%
Beas2B-Parental-aH3K4me3-131,844,60931,245,22498.12%
Beas2B-Parental-aH3K4me3-229,145,75428,620,85098.20%
Beas2B-Parental-aHA-130,090,33329,493,76698.02%
Beas2B-Parental-aHA-229,573,81029,026,74398.15%
Beas2B-H3WT-HA-aH3-130,300,14529,573,35797.60%
Beas2B-H3WT-HA-aH3-234,536,72933,720,40697.64%
Beas2B-H3WT-HA-aIgG-137,079,34036,473,76198.37%
Beas2B-H3WT-HA-aIgG-235,354,69634,667,07598.06%
Beas2B-H3WT-HA-aH3K4me3-138,235,95237,473,02798.00%
Beas2B-H3WT-HA-aH3K4me3-236,649,27635,903,36597.96%
Beas2B-H3WT-HA-aHA-136,560,48835,740,49897.76%
Beas2B-H3WT-HA-aHA-240,144,17839,243,65097.76%
Beas2B-H3E97K-HA-Clone19-aH3-140,831,49240,118,11498.25%
Beas2B-H3E97K-HA-Clone19-aH3-239,806,74239,079,95698.17%
Beas2B-H3E97K-HA-Clone19-aIgG-122,505,25622,114,47898.26%
Beas2B-H3E97K-HA-Clone19-aIgG-221,527,84521,155,39298.27%
Beas2B-H3E97K-HA-Clone19-aH3K4me3-123,892,49223,378,91697.85%
Beas2B-H3E97K-HA-Clone19-aH3K4me3-227,196,36426,606,16697.83%
Beas2B-H3E97K-HA-Clone19-aHA-125,397,92725,016,44598.50%
Beas2B-H3E97K-HA-Clone19-aHA-220,383,74220,040,09098.31%
Beas2B-H3E97K-HA-Clone22-aH3-127,067,76826,550,56398.09%
Beas2B-H3E97K-HA-Clone22-aH3-229,416,58828,876,69798.16%
Beas2B-H3E97K-HA-Clone22-aIgG-130,213,44029,577,00397.89%
Beas2B-H3E97K-HA-Clone22-aIgG-232,936,47932,235,75597.87%
Beas2B-H3E97K-HA-Clone22-aH3K4me3-130,839,12630,340,76798.38%
Beas2B-H3E97K-HA-Clone22-aH3K4me3-230,509,68429,964,89598.21%
Beas2B-H3E97K-HA-Clone22-aHA-136,608,03435,900,63498.07%
Beas2B-H3E97K-HA-Clone22-aHA-232,732,61832,118,68198.12%
Beas2B-H3E97K-HA-Clone23-aH3-120,421,82420,056,12798.21%
Beas2B-H3E97K-HA-Clone23-aH3-219,850,12519,516,81398.32%
Beas2B-H3E97K-HA-Clone23-aIgG-126,922,23726,379,63397.98%
Beas2B-H3E97K-HA-Clone23-aIgG-226,816,57926,315,38098.13%
Beas2B-H3E97K-HA-Clone23-aH3K4me3-129,340,74228,743,55697.96%
Beas2B-H3E97K-HA-Clone23-aH3K4me3-230,080,44829,455,73997.92%
Beas2B-H3E97K-HA-Clone23-aHA-133,986,24433,263,03397.87%
Beas2B-H3E97K-HA-Clone23-aHA-229,423,85428,866,31598.11%
Table 4. Number of reads in each sample before and after QC.



ConditionReads before QCReads after QC% Retained
Beas2B-Parental-aH362,979,52561,799,27598.13%
Beas2B-Parental-aH3K4me360,990,36359,866,07498.16%
Beas2B-Parental-aHA59,664,14358,520,50998.08%
Beas2B-H3WT-HA-aH364,836,87463,293,76397.62%
Beas2B-H3WT-HA-aH3K4me374,885,22873,376,39297.99%
Beas2B-H3WT-HA-aHA76,704,66674,984,14897.76%
Beas2B-H3E97K-HA-Clone19-aH380,638,23479,198,07098.21%
Beas2B-H3E97K-HA-Clone19-aH3K4me351,088,85649,985,08297.84%
Beas2B-H3E97K-HA-Clone19-aHA45,781,66945,056,53598.42%
Beas2B-H3E97K-HA-Clone22-aH356,484,35655,427,26098.13%
Beas2B-H3E97K-HA-Clone22-aH3K4me361,348,81060,305,66298.30%
Beas2B-H3E97K-HA-Clone22-aHA69,340,65268,019,31598.09%
Beas2B-H3E97K-HA-Clone23-aH340,271,94939,572,94098.26%
Beas2B-H3E97K-HA-Clone23-aH3K4me359,421,19058,199,29597.94%
Beas2B-H3E97K-HA-Clone23-aHA63,410,09862,129,34897.98%
Table 5. Number of reads in each condition before and after QC.

3. Mapping to genome
The input sequences were aligned to the hg38 genome using Bowtie 2.4.2. 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
Beas2B-Parental-aH3-126,719,18915,694,53358.74%bam.bowtie/Beas2B-Parental-aH3-1.bt2stats.html
Beas2B-Parental-aH3-235,080,08618,146,12551.73%bam.bowtie/Beas2B-Parental-aH3-2.bt2stats.html
Beas2B-Parental-aIgG-133,263,03319,263,68957.91%bam.bowtie/Beas2B-Parental-aIgG-1.bt2stats.html
Beas2B-Parental-aIgG-228,866,31514,864,79251.50%bam.bowtie/Beas2B-Parental-aIgG-2.bt2stats.html
Beas2B-Parental-aH3K4me3-131,816,19323,423,07073.62%bam.bowtie/Beas2B-Parental-aH3K4me3-1.bt2stats.html
Beas2B-Parental-aH3K4me3-235,822,59722,737,85263.47%bam.bowtie/Beas2B-Parental-aH3K4me3-2.bt2stats.html
Beas2B-Parental-aHA-131,245,22418,197,11258.24%bam.bowtie/Beas2B-Parental-aHA-1.bt2stats.html
Beas2B-Parental-aHA-228,620,85015,596,76354.49%bam.bowtie/Beas2B-Parental-aHA-2.bt2stats.html
Beas2B-H3WT-HA-aH3-129,493,76616,989,99357.61%bam.bowtie/Beas2B-H3WT-HA-aH3-1.bt2stats.html
Beas2B-H3WT-HA-aH3-229,026,74315,357,36652.91%bam.bowtie/Beas2B-H3WT-HA-aH3-2.bt2stats.html
Beas2B-H3WT-HA-aIgG-128,743,55614,530,87150.55%bam.bowtie/Beas2B-H3WT-HA-aIgG-1.bt2stats.html
Beas2B-H3WT-HA-aIgG-229,455,73917,836,07560.55%bam.bowtie/Beas2B-H3WT-HA-aIgG-2.bt2stats.html
Beas2B-H3WT-HA-aH3K4me3-129,573,35720,248,75268.47%bam.bowtie/Beas2B-H3WT-HA-aH3K4me3-1.bt2stats.html
Beas2B-H3WT-HA-aH3K4me3-233,720,40623,152,76968.66%bam.bowtie/Beas2B-H3WT-HA-aH3K4me3-2.bt2stats.html
Beas2B-H3WT-HA-aHA-136,473,76122,647,86762.09%bam.bowtie/Beas2B-H3WT-HA-aHA-1.bt2stats.html
Beas2B-H3WT-HA-aHA-234,667,07525,894,58874.70%bam.bowtie/Beas2B-H3WT-HA-aHA-2.bt2stats.html
Beas2B-H3E97K-HA-Clone19-aH3-137,473,02719,088,00950.94%bam.bowtie/Beas2B-H3E97K-HA-Clone19-aH3-1.bt2stats.html
Beas2B-H3E97K-HA-Clone19-aH3-235,903,36519,570,71754.51%bam.bowtie/Beas2B-H3E97K-HA-Clone19-aH3-2.bt2stats.html
Beas2B-H3E97K-HA-Clone19-aIgG-135,900,63417,834,57349.68%bam.bowtie/Beas2B-H3E97K-HA-Clone19-aIgG-1.bt2stats.html
Beas2B-H3E97K-HA-Clone19-aIgG-232,118,68115,832,63749.29%bam.bowtie/Beas2B-H3E97K-HA-Clone19-aIgG-2.bt2stats.html
Beas2B-H3E97K-HA-Clone19-aH3K4me3-135,740,49824,611,27868.86%bam.bowtie/Beas2B-H3E97K-HA-Clone19-aH3K4me3-1.bt2stats.html
Beas2B-H3E97K-HA-Clone19-aH3K4me3-239,243,65025,176,17764.15%bam.bowtie/Beas2B-H3E97K-HA-Clone19-aH3K4me3-2.bt2stats.html
Beas2B-H3E97K-HA-Clone19-aHA-140,118,11421,525,59653.66%bam.bowtie/Beas2B-H3E97K-HA-Clone19-aHA-1.bt2stats.html
Beas2B-H3E97K-HA-Clone19-aHA-239,079,95622,327,82857.13%bam.bowtie/Beas2B-H3E97K-HA-Clone19-aHA-2.bt2stats.html
Beas2B-H3E97K-HA-Clone22-aH3-122,114,47810,164,17445.96%bam.bowtie/Beas2B-H3E97K-HA-Clone22-aH3-1.bt2stats.html
Beas2B-H3E97K-HA-Clone22-aH3-221,155,39210,151,05747.98%bam.bowtie/Beas2B-H3E97K-HA-Clone22-aH3-2.bt2stats.html
Beas2B-H3E97K-HA-Clone22-aIgG-120,056,1278,166,49540.72%bam.bowtie/Beas2B-H3E97K-HA-Clone22-aIgG-1.bt2stats.html
Beas2B-H3E97K-HA-Clone22-aIgG-219,516,8138,468,29643.39%bam.bowtie/Beas2B-H3E97K-HA-Clone22-aIgG-2.bt2stats.html
Beas2B-H3E97K-HA-Clone22-aH3K4me3-123,378,91616,158,39169.12%bam.bowtie/Beas2B-H3E97K-HA-Clone22-aH3K4me3-1.bt2stats.html
Beas2B-H3E97K-HA-Clone22-aH3K4me3-226,606,16618,353,66668.98%bam.bowtie/Beas2B-H3E97K-HA-Clone22-aH3K4me3-2.bt2stats.html
Beas2B-H3E97K-HA-Clone22-aHA-125,016,44513,292,39453.13%bam.bowtie/Beas2B-H3E97K-HA-Clone22-aHA-1.bt2stats.html
Beas2B-H3E97K-HA-Clone22-aHA-220,040,09010,387,62251.83%bam.bowtie/Beas2B-H3E97K-HA-Clone22-aHA-2.bt2stats.html
Beas2B-H3E97K-HA-Clone23-aH3-126,550,56311,237,17442.32%bam.bowtie/Beas2B-H3E97K-HA-Clone23-aH3-1.bt2stats.html
Beas2B-H3E97K-HA-Clone23-aH3-228,876,69714,221,49549.25%bam.bowtie/Beas2B-H3E97K-HA-Clone23-aH3-2.bt2stats.html
Beas2B-H3E97K-HA-Clone23-aIgG-126,379,63312,799,77348.52%bam.bowtie/Beas2B-H3E97K-HA-Clone23-aIgG-1.bt2stats.html
Beas2B-H3E97K-HA-Clone23-aIgG-226,315,38011,675,08044.37%bam.bowtie/Beas2B-H3E97K-HA-Clone23-aIgG-2.bt2stats.html
Beas2B-H3E97K-HA-Clone23-aH3K4me3-129,577,00319,553,44766.11%bam.bowtie/Beas2B-H3E97K-HA-Clone23-aH3K4me3-1.bt2stats.html
Beas2B-H3E97K-HA-Clone23-aH3K4me3-232,235,75519,908,41561.76%bam.bowtie/Beas2B-H3E97K-HA-Clone23-aH3K4me3-2.bt2stats.html
Beas2B-H3E97K-HA-Clone23-aHA-130,340,76717,788,19658.63%bam.bowtie/Beas2B-H3E97K-HA-Clone23-aHA-1.bt2stats.html
Beas2B-H3E97K-HA-Clone23-aHA-229,964,89517,050,26656.90%bam.bowtie/Beas2B-H3E97K-HA-Clone23-aHA-2.bt2stats.html
Table 6. Number of alignments to genome.

4. Spike-ins normalization
The following table shows the values used to normalize samples on the basis of Spike-ins. The Spike-in reads column contains the number of reads aligning to the genome of the spike-ins, and Spike-in % shows what fraction this represents of the total number of reads. The Scale factor column contains the ratio between the number of Spike-in reads for each sample and the smallest value in that column. This factor is used to scale the input datasets, in order to obtain the same number of spike-in reads in each sample.

SampleTotal readsSpike-in readsSpike-in %Scale factor
Beas2B-Parental-aH3-126,719,1891,066,8073.990.15
Beas2B-Parental-aH3-235,080,0861,724,2994.920.09
Beas2B-Parental-aIgG-133,263,0331,336,9074.020.12
Beas2B-Parental-aIgG-228,866,3151,323,8624.590.12
Beas2B-Parental-aH3K4me3-131,816,193489,0411.540.33
Beas2B-Parental-aH3K4me3-235,822,597621,6391.740.26
Beas2B-Parental-aHA-131,245,2241,743,8115.580.09
Beas2B-Parental-aHA-228,620,8501,734,3706.060.09
Beas2B-H3WT-HA-aH3-129,493,766950,4503.220.17
Beas2B-H3WT-HA-aH3-229,026,743855,4402.950.19
Beas2B-H3WT-HA-aIgG-128,743,5561,124,3833.910.14
Beas2B-H3WT-HA-aIgG-229,455,739645,0782.190.25
Beas2B-H3WT-HA-aH3K4me3-129,573,357301,5751.020.53
Beas2B-H3WT-HA-aH3K4me3-233,720,406450,9721.340.35
Beas2B-H3WT-HA-aHA-136,473,761201,0300.550.79
Beas2B-H3WT-HA-aHA-234,667,075160,2680.460.99
Beas2B-H3E97K-HA-Clone19-aH3-137,473,0271,222,5833.260.13
Beas2B-H3E97K-HA-Clone19-aH3-235,903,3651,078,7213.000.15
Beas2B-H3E97K-HA-Clone19-aIgG-135,900,634858,0062.390.19
Beas2B-H3E97K-HA-Clone19-aIgG-232,118,681855,1992.660.19
Beas2B-H3E97K-HA-Clone19-aH3K4me3-135,740,498369,0891.030.43
Beas2B-H3E97K-HA-Clone19-aH3K4me3-239,243,650344,8560.880.46
Beas2B-H3E97K-HA-Clone19-aHA-140,118,114568,5251.420.28
Beas2B-H3E97K-HA-Clone19-aHA-239,079,956761,5631.950.21
Beas2B-H3E97K-HA-Clone22-aH3-122,114,478697,8713.160.23
Beas2B-H3E97K-HA-Clone22-aH3-221,155,392366,5101.730.43
Beas2B-H3E97K-HA-Clone22-aIgG-120,056,127699,0633.490.23
Beas2B-H3E97K-HA-Clone22-aIgG-219,516,813794,8034.070.20
Beas2B-H3E97K-HA-Clone22-aH3K4me3-123,378,916159,3880.681.00
Beas2B-H3E97K-HA-Clone22-aH3K4me3-226,606,166265,7471.000.60
Beas2B-H3E97K-HA-Clone22-aHA-125,016,445563,3502.250.28
Beas2B-H3E97K-HA-Clone22-aHA-220,040,090386,5551.930.41
Beas2B-H3E97K-HA-Clone23-aH3-126,550,563763,0762.870.21
Beas2B-H3E97K-HA-Clone23-aH3-228,876,697675,6422.340.24
Beas2B-H3E97K-HA-Clone23-aIgG-126,379,633609,4002.310.26
Beas2B-H3E97K-HA-Clone23-aIgG-226,315,380814,5113.100.20
Beas2B-H3E97K-HA-Clone23-aH3K4me3-129,577,003216,4180.730.74
Beas2B-H3E97K-HA-Clone23-aH3K4me3-232,235,755252,7000.780.63
Beas2B-H3E97K-HA-Clone23-aHA-130,340,767456,5981.500.35
Beas2B-H3E97K-HA-Clone23-aHA-229,964,895470,8401.570.34
Table 7. Spike-in normalization results

5. 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
Beas2B-Parental-aH3-1123,187,3180.048,377,4240.30%14.70
Beas2B-Parental-aH3-2283,398,8390.0925,343,5860.80%11.18
Beas2B-Parental-aIgG-187,980,9340.036,025,3020.20%14.60
Beas2B-Parental-aIgG-2114,588,1320.047,514,3800.20%15.25
Beas2B-Parental-aH3K4me3-12,087,001,8190.6835,483,3601.10%58.82
Beas2B-Parental-aH3K4me3-22,468,029,0450.8037,988,4241.20%64.97
Beas2B-Parental-aHA-1113,673,4260.047,684,4510.20%14.79
Beas2B-Parental-aHA-2108,412,2310.047,368,4580.20%14.71
Beas2B-H3WT-HA-aH3-1152,499,4260.0511,154,1710.40%13.67
Beas2B-H3WT-HA-aH3-2148,201,3250.0510,684,0720.30%13.87
Beas2B-H3WT-HA-aIgG-1114,197,9480.047,957,4670.30%14.35
Beas2B-H3WT-HA-aIgG-2125,610,4040.048,569,9150.30%14.66
Beas2B-H3WT-HA-aH3K4me3-11,142,229,3140.3733,327,0061.10%34.27
Beas2B-H3WT-HA-aH3K4me3-21,603,658,2140.5235,632,1531.20%45.01
Beas2B-H3WT-HA-aHA-1706,127,9060.2389,937,9352.90%7.85
Beas2B-H3WT-HA-aHA-2102,022,7910.038,508,7400.30%11.99
Beas2B-H3E97K-HA-Clone19-aH3-1314,310,7100.1029,170,0630.90%10.78
Beas2B-H3E97K-HA-Clone19-aH3-2233,038,4760.0819,178,1100.60%12.15
Beas2B-H3E97K-HA-Clone19-aIgG-1303,628,8910.1028,465,4110.90%10.67
Beas2B-H3E97K-HA-Clone19-aIgG-2200,304,9990.0616,717,3070.50%11.98
Beas2B-H3E97K-HA-Clone19-aH3K4me3-11,740,728,1290.5641,102,0861.30%42.35
Beas2B-H3E97K-HA-Clone19-aH3K4me3-21,921,514,6720.6246,507,3361.50%41.32
Beas2B-H3E97K-HA-Clone19-aHA-1718,459,0300.2383,707,7842.70%8.58
Beas2B-H3E97K-HA-Clone19-aHA-2481,137,8630.1652,149,6291.70%9.23
Beas2B-H3E97K-HA-Clone22-aH3-197,326,3690.036,750,2390.20%14.42
Beas2B-H3E97K-HA-Clone22-aH3-2103,733,9140.037,451,7990.20%13.92
Beas2B-H3E97K-HA-Clone22-aIgG-1123,711,0130.0410,030,8100.30%12.33
Beas2B-H3E97K-HA-Clone22-aIgG-286,120,5600.035,936,8470.20%14.51
Beas2B-H3E97K-HA-Clone22-aH3K4me3-12,227,402,9970.7236,473,9831.20%61.07
Beas2B-H3E97K-HA-Clone22-aH3K4me3-21,602,236,4550.5235,480,8601.10%45.16
Beas2B-H3E97K-HA-Clone22-aHA-1133,936,2910.0410,652,3330.30%12.57
Beas2B-H3E97K-HA-Clone22-aHA-2213,558,0110.0722,479,4980.70%9.50
Beas2B-H3E97K-HA-Clone23-aH3-1215,099,2050.0720,885,1770.70%10.30
Beas2B-H3E97K-HA-Clone23-aH3-2284,033,8260.0927,911,5270.90%10.18
Beas2B-H3E97K-HA-Clone23-aIgG-1121,222,0020.048,800,3680.30%13.77
Beas2B-H3E97K-HA-Clone23-aIgG-2109,842,9460.047,951,3020.30%13.81
Beas2B-H3E97K-HA-Clone23-aH3K4me3-11,924,674,7830.6243,404,4871.40%44.34
Beas2B-H3E97K-HA-Clone23-aH3K4me3-21,931,322,1650.6342,531,4881.40%45.41
Beas2B-H3E97K-HA-Clone23-aHA-1326,894,8090.1134,839,8511.10%9.38
Beas2B-H3E97K-HA-Clone23-aHA-2542,723,7640.1864,507,1732.10%8.41
Table 8. Genome coverage by sample.

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

NameTotal ntCoverageEffective bpEffective PercEff Coverage
Beas2B-Parental-aH3722,485,8230.2373,294,7992.40%9.86
Beas2B-Parental-aH3K4me300.0000.00%0.00
Beas2B-Parental-aHA335,721,6060.1126,913,5660.90%12.47
Beas2B-H3WT-HA-aH3508,738,5170.1646,309,0871.50%10.99
Beas2B-H3WT-HA-aH3K4me32,857,548,3550.9352,882,9351.70%54.04
Beas2B-H3WT-HA-aHA00.0000.00%0.00
Beas2B-H3E97K-HA-Clone19-aH31,145,539,7440.37125,394,6394.10%9.14
Beas2B-H3E97K-HA-Clone19-aH3K4me300.0000.00%0.00
Beas2B-H3E97K-HA-Clone19-aHA00.0000.00%0.00
Beas2B-H3E97K-HA-Clone22-aH3326,913,6680.1128,874,7520.90%11.32
Beas2B-H3E97K-HA-Clone22-aH3K4me33,922,432,5921.2751,378,6141.70%76.34
Beas2B-H3E97K-HA-Clone22-aHA673,940,8200.2274,584,6472.40%9.04
Beas2B-H3E97K-HA-Clone23-aH31,146,728,4310.37134,639,2144.40%8.52
Beas2B-H3E97K-HA-Clone23-aH3K4me34,014,602,9871.3068,950,1852.20%58.22
Beas2B-H3E97K-HA-Clone23-aHA2,048,242,8760.66249,405,9388.10%8.21
Table 9. Genome coverage by condition

File: NS3570.sample.cov.xlsx
Size: 93.48 kB
Description: Per-chromosome coverage data, by sample.

File: NS3570.cond.cov.xlsx
Size: 31.73 kB
Description: Per-chromosome coverage data, by condition.

6. Peak detection
Peak detection was performed using SEACR with the following options: mode=stringent, normalization=False. The following table shows the number of peaks found for each condition.

ConditionTotal PeaksPeaksActions
Beas2B-Parental-aH3143,645Beas2B-Parental-aH3.peaks.bedCreate RegionSet
Beas2B-Parental-aH3K4me37,548Beas2B-Parental-aH3K4me3.peaks.bedCreate RegionSet
Beas2B-Parental-aHA12,355Beas2B-Parental-aHA.peaks.bedCreate RegionSet
Beas2B-H3WT-HA-aH32,746Beas2B-H3WT-HA-aH3.peaks.bedCreate RegionSet
Beas2B-H3WT-HA-aH3K4me37,585Beas2B-H3WT-HA-aH3K4me3.peaks.bedCreate RegionSet
Beas2B-H3WT-HA-aHA94,356Beas2B-H3WT-HA-aHA.peaks.bedCreate RegionSet
Beas2B-H3E97K-HA-Clone19-aH30Beas2B-H3E97K-HA-Clone19-aH3.peaks.bedCreate RegionSet
Beas2B-H3E97K-HA-Clone19-aH3K4me37,957Beas2B-H3E97K-HA-Clone19-aH3K4me3.peaks.bedCreate RegionSet
Beas2B-H3E97K-HA-Clone19-aHA6,360Beas2B-H3E97K-HA-Clone19-aHA.peaks.bedCreate RegionSet
Beas2B-H3E97K-HA-Clone22-aH3529Beas2B-H3E97K-HA-Clone22-aH3.peaks.bedCreate RegionSet
Beas2B-H3E97K-HA-Clone22-aH3K4me33,331Beas2B-H3E97K-HA-Clone22-aH3K4me3.peaks.bedCreate RegionSet
Beas2B-H3E97K-HA-Clone22-aHA6,341Beas2B-H3E97K-HA-Clone22-aHA.peaks.bedCreate RegionSet
Beas2B-H3E97K-HA-Clone23-aH36,186Beas2B-H3E97K-HA-Clone23-aH3.peaks.bedCreate RegionSet
Beas2B-H3E97K-HA-Clone23-aH3K4me33,930Beas2B-H3E97K-HA-Clone23-aH3K4me3.peaks.bedCreate RegionSet
Beas2B-H3E97K-HA-Clone23-aHA6,093Beas2B-H3E97K-HA-Clone23-aHA.peaks.bedCreate RegionSet
Table 10. Peaks detected by SEACR and their classification in genomic regions.

The following histogram shows the distribution of peak locations in the different conditions.
File: peak-classifications.xlsx
Size: 6.22 kB
Description: Table containing number of peaks in each region for each condition.

7. 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
Beas2B-Parental-aH394,712,5723,471,7053.67%
Beas2B-Parental-aH3K4me3109,214,44771,614,07365.57%
Beas2B-Parental-aHA92,870,917463,9130.50%
Beas2B-H3WT-HA-aH391,197,460119,9220.13%
Beas2B-H3WT-HA-aH3K4me3105,320,24655,097,25452.31%
Beas2B-H3WT-HA-aHA125,095,0967,925,2556.34%
Beas2B-H3E97K-HA-Clone19-aH3110,851,68100.00%
Beas2B-H3E97K-HA-Clone19-aH3K4me3124,158,01761,589,50649.61%
Beas2B-H3E97K-HA-Clone19-aHA123,483,8171,134,9440.92%
Beas2B-H3E97K-HA-Clone22-aH362,353,13857,2670.09%
Beas2B-H3E97K-HA-Clone22-aH3K4me383,795,81032,035,57938.23%
Beas2B-H3E97K-HA-Clone22-aHA69,292,125638,8390.92%
Beas2B-H3E97K-HA-Clone23-aH377,643,403190,0670.24%
Beas2B-H3E97K-HA-Clone23-aH3K4me397,254,13637,400,89338.46%
Beas2B-H3E97K-HA-Clone23-aHA96,883,757815,7210.84%
Table 11. Fraction of Reads in Peaks

8. Differential peak detection
The following table reports peaks that are increased, decreased, or unchanged in each contrast. Note that these results are simply based on the fold change of the peak sizes in the two conditions, with no statistical significance information, using a Log2(FC) threshold of 1.0. More accurate differential analysis can be performed with DASA.

TestControlTotalIncreasedDecreasedUnchangedTable
Beas2B-H3WT-HA-aH3Beas2B-Parental-aH36172%8%19%Beas2B-H3WT-HA-aH3.vs.Beas2B-Parental-aH3.xlsx
Beas2B-H3E97K-HA-Clone19-aH3Beas2B-Parental-aH300%0%0%Beas2B-H3E97K-HA-Clone19-aH3.vs.Beas2B-Parental-aH3.xlsx
Beas2B-H3E97K-HA-Clone22-aH3Beas2B-Parental-aH35100%0%0%Beas2B-H3E97K-HA-Clone22-aH3.vs.Beas2B-Parental-aH3.xlsx
Beas2B-H3E97K-HA-Clone23-aH3Beas2B-Parental-aH313226%50%23%Beas2B-H3E97K-HA-Clone23-aH3.vs.Beas2B-Parental-aH3.xlsx
Beas2B-H3WT-HA-aH3K4me3Beas2B-Parental-aH3K4me37,0601%1%96%Beas2B-H3WT-HA-aH3K4me3.vs.Beas2B-Parental-aH3K4me3.xlsx
Beas2B-H3E97K-HA-Clone19-aH3K4me3Beas2B-Parental-aH3K4me37,0922%2%95%Beas2B-H3E97K-HA-Clone19-aH3K4me3.vs.Beas2B-Parental-aH3K4me3.xlsx
Beas2B-H3E97K-HA-Clone22-aH3K4me3Beas2B-Parental-aH3K4me33,28333%0%65%Beas2B-H3E97K-HA-Clone22-aH3K4me3.vs.Beas2B-Parental-aH3K4me3.xlsx
Beas2B-H3E97K-HA-Clone23-aH3K4me3Beas2B-Parental-aH3K4me33,83117%0%82%Beas2B-H3E97K-HA-Clone23-aH3K4me3.vs.Beas2B-Parental-aH3K4me3.xlsx
Beas2B-H3WT-HA-aHABeas2B-Parental-aHA36295%2%2%Beas2B-H3WT-HA-aHA.vs.Beas2B-Parental-aHA.xlsx
Beas2B-H3E97K-HA-Clone19-aHABeas2B-Parental-aHA2696%0%3%Beas2B-H3E97K-HA-Clone19-aHA.vs.Beas2B-Parental-aHA.xlsx
Beas2B-H3E97K-HA-Clone22-aHABeas2B-Parental-aHA11100%0%0%Beas2B-H3E97K-HA-Clone22-aHA.vs.Beas2B-Parental-aHA.xlsx
Beas2B-H3E97K-HA-Clone23-aHABeas2B-Parental-aHA21100%0%0%Beas2B-H3E97K-HA-Clone23-aHA.vs.Beas2B-Parental-aHA.xlsx
Beas2B-H3E97K-HA-Clone19-aHABeas2B-H3WT-HA-aHA3,44731%30%37%Beas2B-H3E97K-HA-Clone19-aHA.vs.Beas2B-H3WT-HA-aHA.xlsx
Beas2B-H3E97K-HA-Clone22-aHABeas2B-H3WT-HA-aHA2,4857%75%17%Beas2B-H3E97K-HA-Clone22-aHA.vs.Beas2B-H3WT-HA-aHA.xlsx
Beas2B-H3E97K-HA-Clone23-aHABeas2B-H3WT-HA-aHA3,07617%45%37%Beas2B-H3E97K-HA-Clone23-aHA.vs.Beas2B-H3WT-HA-aHA.xlsx
Beas2B-H3E97K-HA-Clone19-aH3Beas2B-H3WT-HA-aH300%0%0%Beas2B-H3E97K-HA-Clone19-aH3.vs.Beas2B-H3WT-HA-aH3.xlsx
Beas2B-H3E97K-HA-Clone22-aH3Beas2B-H3WT-HA-aH300%0%0%Beas2B-H3E97K-HA-Clone22-aH3.vs.Beas2B-H3WT-HA-aH3.xlsx
Beas2B-H3E97K-HA-Clone23-aH3Beas2B-H3WT-HA-aH3616%83%0%Beas2B-H3E97K-HA-Clone23-aH3.vs.Beas2B-H3WT-HA-aH3.xlsx
Beas2B-H3E97K-HA-Clone19-aH3K4me3Beas2B-H3WT-HA-aH3K4me37,3271%1%97%Beas2B-H3E97K-HA-Clone19-aH3K4me3.vs.Beas2B-H3WT-HA-aH3K4me3.xlsx
Beas2B-H3E97K-HA-Clone22-aH3K4me3Beas2B-H3WT-HA-aH3K4me33,33027%0%72%Beas2B-H3E97K-HA-Clone22-aH3K4me3.vs.Beas2B-H3WT-HA-aH3K4me3.xlsx
Beas2B-H3E97K-HA-Clone23-aH3K4me3Beas2B-H3WT-HA-aH3K4me33,92911%0%88%Beas2B-H3E97K-HA-Clone23-aH3K4me3.vs.Beas2B-H3WT-HA-aH3K4me3.xlsx
Show values | percentages
Table 12. Differential peak analysis results.

The following table reports the number of increased and decreased peaks that belong to enhancers.

TestControlInc - PeaksInc - EnhancersDec - PeaksDec - EnhancersTable
Beas2B-H3WT-HA-aH3Beas2B-Parental-aH30000Beas2B-H3WT-HA-aH3.vs.Beas2B-Parental-aH3.enhancers.xlsx
Beas2B-H3E97K-HA-Clone19-aH3Beas2B-Parental-aH30000Beas2B-H3E97K-HA-Clone19-aH3.vs.Beas2B-Parental-aH3.enhancers.xlsx
Beas2B-H3E97K-HA-Clone22-aH3Beas2B-Parental-aH30000Beas2B-H3E97K-HA-Clone22-aH3.vs.Beas2B-Parental-aH3.enhancers.xlsx
Beas2B-H3E97K-HA-Clone23-aH3Beas2B-Parental-aH33322Beas2B-H3E97K-HA-Clone23-aH3.vs.Beas2B-Parental-aH3.enhancers.xlsx
Beas2B-H3WT-HA-aH3K4me3Beas2B-Parental-aH3K4me36677Beas2B-H3WT-HA-aH3K4me3.vs.Beas2B-Parental-aH3K4me3.enhancers.xlsx
Beas2B-H3E97K-HA-Clone19-aH3K4me3Beas2B-Parental-aH3K4me310141111Beas2B-H3E97K-HA-Clone19-aH3K4me3.vs.Beas2B-Parental-aH3K4me3.enhancers.xlsx
Beas2B-H3E97K-HA-Clone22-aH3K4me3Beas2B-Parental-aH3K4me3739311Beas2B-H3E97K-HA-Clone22-aH3K4me3.vs.Beas2B-Parental-aH3K4me3.enhancers.xlsx
Beas2B-H3E97K-HA-Clone23-aH3K4me3Beas2B-Parental-aH3K4me3385000Beas2B-H3E97K-HA-Clone23-aH3K4me3.vs.Beas2B-Parental-aH3K4me3.enhancers.xlsx
Beas2B-H3WT-HA-aHABeas2B-Parental-aHA121111Beas2B-H3WT-HA-aHA.vs.Beas2B-Parental-aHA.enhancers.xlsx
Beas2B-H3E97K-HA-Clone19-aHABeas2B-Parental-aHA0000Beas2B-H3E97K-HA-Clone19-aHA.vs.Beas2B-Parental-aHA.enhancers.xlsx
Beas2B-H3E97K-HA-Clone22-aHABeas2B-Parental-aHA0000Beas2B-H3E97K-HA-Clone22-aHA.vs.Beas2B-Parental-aHA.enhancers.xlsx
Beas2B-H3E97K-HA-Clone23-aHABeas2B-Parental-aHA1100Beas2B-H3E97K-HA-Clone23-aHA.vs.Beas2B-Parental-aHA.enhancers.xlsx
Beas2B-H3E97K-HA-Clone19-aHABeas2B-H3WT-HA-aHA20192423Beas2B-H3E97K-HA-Clone19-aHA.vs.Beas2B-H3WT-HA-aHA.enhancers.xlsx
Beas2B-H3E97K-HA-Clone22-aHABeas2B-H3WT-HA-aHA776460Beas2B-H3E97K-HA-Clone22-aHA.vs.Beas2B-H3WT-HA-aHA.enhancers.xlsx
Beas2B-H3E97K-HA-Clone23-aHABeas2B-H3WT-HA-aHA16143938Beas2B-H3E97K-HA-Clone23-aHA.vs.Beas2B-H3WT-HA-aHA.enhancers.xlsx
Beas2B-H3E97K-HA-Clone19-aH3Beas2B-H3WT-HA-aH30000Beas2B-H3E97K-HA-Clone19-aH3.vs.Beas2B-H3WT-HA-aH3.enhancers.xlsx
Beas2B-H3E97K-HA-Clone22-aH3Beas2B-H3WT-HA-aH30000Beas2B-H3E97K-HA-Clone22-aH3.vs.Beas2B-H3WT-HA-aH3.enhancers.xlsx
Beas2B-H3E97K-HA-Clone23-aH3Beas2B-H3WT-HA-aH30000Beas2B-H3E97K-HA-Clone23-aH3.vs.Beas2B-H3WT-HA-aH3.enhancers.xlsx
Beas2B-H3E97K-HA-Clone19-aH3K4me3Beas2B-H3WT-HA-aH3K4me381144Beas2B-H3E97K-HA-Clone19-aH3K4me3.vs.Beas2B-H3WT-HA-aH3K4me3.enhancers.xlsx
Beas2B-H3E97K-HA-Clone22-aH3K4me3Beas2B-H3WT-HA-aH3K4me3566700Beas2B-H3E97K-HA-Clone22-aH3K4me3.vs.Beas2B-H3WT-HA-aH3K4me3.enhancers.xlsx
Beas2B-H3E97K-HA-Clone23-aH3K4me3Beas2B-H3WT-HA-aH3K4me3212600Beas2B-H3E97K-HA-Clone23-aH3K4me3.vs.Beas2B-H3WT-HA-aH3K4me3.enhancers.xlsx
Table 13. Differential peaks in enhancers.

9. 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
10. UCSC hub

UCSC Genome Browser: use the previous link to display the data tracks automatically, or copy the the URL https://bw:bw@lichtlab.cancer.ufl.edu/reports/H2B//NS3570/NS3570/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: https://bw:bw@lichtlab.cancer.ufl.edu/reports/H2B//NS3570/NS3570/hub.json.



Completed: 1-9-2024@5:37
© 2024, A. Riva, University of Florida.