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Cut&Run - Alignment and peak finding

Title: H2B_CR_20230613
Project: (none)
Started on: 6/20/2023 23:20:05
Hostname: login1.ufhpc
Run directory: /blue/licht/runs/H2B-E77K-Project/H2B_CR_20230613/H2B_CR_20230613
Configuration H2B_CR_20230613.conf

Table of contents:

Input data
Trimming and quality control
Mapping to genome
Genome coverage
Peak detection
Fraction of Reads in Peaks
Differential peak detection
MultiQC report
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).

Category	Data
*Summary of input data*
Experimental conditions:	WT-H3K27ac, HET-H3K27ac, WT-H3K27me3, HET-H3K27me3, WT-H3K4me3, HET-H3K4me3, WT-HA, HET-HA
Contrasts:	HET-H3K27ac vs. WT-H3K27ac, HET-H3K27me3 vs. WT-H3K27me3, HET-H3K4me3 vs. WT-H3K4me3, HET-HA vs. WT-HA
Number of samples	28
*Sequencing data data*
Total number of reads:	1,001,274,336
Average reads per sample:	35,759,797

Table 1. Summary of input data

Condition	Sample	Number of reads	% Reads
WT-H3K27ac	WT-H3K27ac-1	36,484,725	3.64%
	WT-H3K27ac-2	39,275,826	3.92%
	WT-H3K27ac-3	37,705,542	3.77%
HET-H3K27ac	HET-H3K27ac-1	29,128,497	2.91%
	HET-H3K27ac-2	30,317,216	3.03%
	HET-H3K27ac-3	34,079,609	3.40%
WT-H3K27me3	WT-H3K27me3-1	38,235,173	3.82%
	WT-H3K27me3-2	40,220,129	4.02%
	WT-H3K27me3-3	39,739,696	3.97%
HET-H3K27me3	HET-H3K27me3-1	33,101,419	3.31%
	HET-H3K27me3-2	39,904,248	3.99%
	HET-H3K27me3-3	33,787,754	3.37%
WT-H3K4me3	WT-H3K4me3-1	35,092,049	3.50%
	WT-H3K4me3-2	31,933,795	3.19%
	WT-H3K4me3-3	35,649,926	3.56%
HET-H3K4me3	HET-H3K4me3-1	26,642,874	2.66%
	HET-H3K4me3-2	30,958,383	3.09%
	HET-H3K4me3-3	26,047,619	2.60%
WT-HA	WT-HA-1	38,976,410	3.89%
WT-HA	WT-HA-2	41,479,767	4.14%
HET-HA	HET-HA-1	39,229,604	3.92%
HET-HA	HET-HA-2	40,773,090	4.07%

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.

Sample	Readset	Reads before trim	QC before trim	Reads after trim	QC after trim	% Retained
WT-H3K27ac-1	WT-H3K27ac-1_r1	36,484,725	WT-H3K27ac_S11_L004_R1_001 WT-H3K27ac_S11_L004_R2_001	35,377,936	WT-H3K27ac_S11_L004_R1_001.trim.paired WT-H3K27ac_S11_L004_R2_001.trim.paired	96.97%
WT-H3K27ac-2	WT-H3K27ac-2_r1	39,275,826	WT-H3K27ac_S12_L004_R1_001 WT-H3K27ac_S12_L004_R2_001	38,001,608	WT-H3K27ac_S12_L004_R1_001.trim.paired WT-H3K27ac_S12_L004_R2_001.trim.paired	96.76%
WT-H3K27ac-3	WT-H3K27ac-3_r1	37,705,542	WT-H3K27ac_S13_L004_R1_001 WT-H3K27ac_S13_L004_R2_001	36,493,684	WT-H3K27ac_S13_L004_R1_001.trim.paired WT-H3K27ac_S13_L004_R2_001.trim.paired	96.79%
WT-IgG-1	WT-IgG-1_r1	38,009,074	WT-IgG_S23_L004_R1_001 WT-IgG_S23_L004_R2_001	36,719,558	WT-IgG_S23_L004_R1_001.trim.paired WT-IgG_S23_L004_R2_001.trim.paired	96.61%
WT-IgG-2	WT-IgG-2_r1	38,847,278	WT-IgG_S24_L004_R1_001 WT-IgG_S24_L004_R2_001	37,426,036	WT-IgG_S24_L004_R1_001.trim.paired WT-IgG_S24_L004_R2_001.trim.paired	96.34%
WT-IgG-3	WT-IgG-3_r1	36,587,783	WT-IgG_S25_L004_R1_001 WT-IgG_S25_L004_R2_001	35,294,530	WT-IgG_S25_L004_R1_001.trim.paired WT-IgG_S25_L004_R2_001.trim.paired	96.47%
HET-H3K27ac-1	HET-H3K27ac-1_r1	29,128,497	HET-H3K27ac_S14_L004_R1_001 HET-H3K27ac_S14_L004_R2_001	28,184,664	HET-H3K27ac_S14_L004_R1_001.trim.paired HET-H3K27ac_S14_L004_R2_001.trim.paired	96.76%
HET-H3K27ac-2	HET-H3K27ac-2_r1	30,317,216	HET-H3K27ac_S15_L004_R1_001 HET-H3K27ac_S15_L004_R2_001	28,984,481	HET-H3K27ac_S15_L004_R1_001.trim.paired HET-H3K27ac_S15_L004_R2_001.trim.paired	95.60%
HET-H3K27ac-3	HET-H3K27ac-3_r1	34,079,609	HET-H3K27ac_S16_L004_R1_001 HET-H3K27ac_S16_L004_R2_001	33,031,969	HET-H3K27ac_S16_L004_R1_001.trim.paired HET-H3K27ac_S16_L004_R2_001.trim.paired	96.93%
HET-IgG-1	HET-IgG-1_r1	34,477,539	HET-IgG_S26_L004_R1_001 HET-IgG_S26_L004_R2_001	33,316,847	HET-IgG_S26_L004_R1_001.trim.paired HET-IgG_S26_L004_R2_001.trim.paired	96.63%
HET-IgG-2	HET-IgG-2_r1	36,164,823	HET-IgG_S27_L004_R1_001 HET-IgG_S27_L004_R2_001	35,073,720	HET-IgG_S27_L004_R1_001.trim.paired HET-IgG_S27_L004_R2_001.trim.paired	96.98%
HET-IgG-3	HET-IgG-3_r1	38,424,488	HET-IgG_S28_L004_R1_001 HET-IgG_S28_L004_R2_001	37,136,094	HET-IgG_S28_L004_R1_001.trim.paired HET-IgG_S28_L004_R2_001.trim.paired	96.65%
WT-H3K27me3-1	WT-H3K27me3-1_r1	38,235,173	WT-H3K27me3_S5_L004_R1_001 WT-H3K27me3_S5_L004_R2_001	36,834,262	WT-H3K27me3_S5_L004_R1_001.trim.paired WT-H3K27me3_S5_L004_R2_001.trim.paired	96.34%
WT-H3K27me3-2	WT-H3K27me3-2_r1	40,220,129	WT-H3K27me3_S6_L004_R1_001 WT-H3K27me3_S6_L004_R2_001	38,716,112	WT-H3K27me3_S6_L004_R1_001.trim.paired WT-H3K27me3_S6_L004_R2_001.trim.paired	96.26%
WT-H3K27me3-3	WT-H3K27me3-3_r1	39,739,696	WT-H3K27me3_S7_L004_R1_001 WT-H3K27me3_S7_L004_R2_001	38,381,932	WT-H3K27me3_S7_L004_R1_001.trim.paired WT-H3K27me3_S7_L004_R2_001.trim.paired	96.58%
HET-H3K27me3-1	HET-H3K27me3-1_r1	33,101,419	HET-H3K27me3_S10_L004_R1_001 HET-H3K27me3_S10_L004_R2_001	32,028,139	HET-H3K27me3_S10_L004_R1_001.trim.paired HET-H3K27me3_S10_L004_R2_001.trim.paired	96.76%
HET-H3K27me3-2	HET-H3K27me3-2_r1	39,904,248	HET-H3K27me3_S8_L004_R1_001 HET-H3K27me3_S8_L004_R2_001	38,568,107	HET-H3K27me3_S8_L004_R1_001.trim.paired HET-H3K27me3_S8_L004_R2_001.trim.paired	96.65%
HET-H3K27me3-3	HET-H3K27me3-3_r1	33,787,754	HET-H3K27me3_S9_L004_R1_001 HET-H3K27me3_S9_L004_R2_001	32,694,911	HET-H3K27me3_S9_L004_R1_001.trim.paired HET-H3K27me3_S9_L004_R2_001.trim.paired	96.77%
WT-H3K4me3-1	WT-H3K4me3-1_r1	35,092,049	WT-H3K4me3_S17_L004_R1_001 WT-H3K4me3_S17_L004_R2_001	33,597,231	WT-H3K4me3_S17_L004_R1_001.trim.paired WT-H3K4me3_S17_L004_R2_001.trim.paired	95.74%
WT-H3K4me3-2	WT-H3K4me3-2_r1	31,933,795	WT-H3K4me3_S18_L004_R1_001 WT-H3K4me3_S18_L004_R2_001	30,586,567	WT-H3K4me3_S18_L004_R1_001.trim.paired WT-H3K4me3_S18_L004_R2_001.trim.paired	95.78%
WT-H3K4me3-3	WT-H3K4me3-3_r1	35,649,926	WT-H3K4me3_S19_L004_R1_001 WT-H3K4me3_S19_L004_R2_001	34,221,746	WT-H3K4me3_S19_L004_R1_001.trim.paired WT-H3K4me3_S19_L004_R2_001.trim.paired	95.99%
HET-H3K4me3-1	HET-H3K4me3-1_r1	26,642,874	HET-H3K4me3_S20_L004_R1_001 HET-H3K4me3_S20_L004_R2_001	25,557,181	HET-H3K4me3_S20_L004_R1_001.trim.paired HET-H3K4me3_S20_L004_R2_001.trim.paired	95.93%
HET-H3K4me3-2	HET-H3K4me3-2_r1	30,958,383	HET-H3K4me3_S21_L004_R1_001 HET-H3K4me3_S21_L004_R2_001	29,651,098	HET-H3K4me3_S21_L004_R1_001.trim.paired HET-H3K4me3_S21_L004_R2_001.trim.paired	95.78%
HET-H3K4me3-3	HET-H3K4me3-3_r1	26,047,619	HET-H3K4me3_S22_L004_R1_001 HET-H3K4me3_S22_L004_R2_001	24,829,827	HET-H3K4me3_S22_L004_R1_001.trim.paired HET-H3K4me3_S22_L004_R2_001.trim.paired	95.32%
WT-HA-1	WT-HA-1_r1	38,976,410	WT-HA_S1_L004_R1_001 WT-HA_S1_L004_R2_001	37,462,024	WT-HA_S1_L004_R1_001.trim.paired WT-HA_S1_L004_R2_001.trim.paired	96.11%
WT-HA-2	WT-HA-2_r1	41,479,767	WT-HA_S2_L004_R1_001 WT-HA_S2_L004_R2_001	40,014,919	WT-HA_S2_L004_R1_001.trim.paired WT-HA_S2_L004_R2_001.trim.paired	96.47%
HET-HA-1	HET-HA-1_r1	39,229,604	HET-HA_S3_L004_R1_001 HET-HA_S3_L004_R2_001	37,719,703	HET-HA_S3_L004_R1_001.trim.paired HET-HA_S3_L004_R2_001.trim.paired	96.15%
HET-HA-2	HET-HA-2_r1	40,773,090	HET-HA_S4_L004_R1_001 HET-HA_S4_L004_R2_001	39,148,037	HET-HA_S4_L004_R1_001.trim.paired HET-HA_S4_L004_R2_001.trim.paired	96.01%

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.

Sample	Reads before QC	Reads after QC	% Retained
WT-H3K27ac-1	36,484,725	35,377,936	96.97%
WT-H3K27ac-2	39,275,826	38,001,608	96.76%
WT-H3K27ac-3	37,705,542	36,493,684	96.79%
WT-IgG-1	38,009,074	36,719,558	96.61%
WT-IgG-2	38,847,278	37,426,036	96.34%
WT-IgG-3	36,587,783	35,294,530	96.47%
HET-H3K27ac-1	29,128,497	28,184,664	96.76%
HET-H3K27ac-2	30,317,216	28,984,481	95.60%
HET-H3K27ac-3	34,079,609	33,031,969	96.93%
HET-IgG-1	34,477,539	33,316,847	96.63%
HET-IgG-2	36,164,823	35,073,720	96.98%
HET-IgG-3	38,424,488	37,136,094	96.65%
WT-H3K27me3-1	38,235,173	36,834,262	96.34%
WT-H3K27me3-2	40,220,129	38,716,112	96.26%
WT-H3K27me3-3	39,739,696	38,381,932	96.58%
HET-H3K27me3-1	33,101,419	32,028,139	96.76%
HET-H3K27me3-2	39,904,248	38,568,107	96.65%
HET-H3K27me3-3	33,787,754	32,694,911	96.77%
WT-H3K4me3-1	35,092,049	33,597,231	95.74%
WT-H3K4me3-2	31,933,795	30,586,567	95.78%
WT-H3K4me3-3	35,649,926	34,221,746	95.99%
HET-H3K4me3-1	26,642,874	25,557,181	95.93%
HET-H3K4me3-2	30,958,383	29,651,098	95.78%
HET-H3K4me3-3	26,047,619	24,829,827	95.32%
WT-HA-1	38,976,410	37,462,024	96.11%
WT-HA-2	41,479,767	40,014,919	96.47%
HET-HA-1	39,229,604	37,719,703	96.15%
HET-HA-2	40,773,090	39,148,037	96.01%

Table 4. Number of reads in each sample before and after QC.

Condition	Reads before QC	Reads after QC	% Retained
WT-H3K27ac	113,466,093	109,873,228	96.83%
HET-H3K27ac	93,525,322	90,201,114	96.45%
WT-H3K27me3	118,194,998	113,932,306	96.39%
HET-H3K27me3	106,793,421	103,291,157	96.72%
WT-H3K4me3	102,675,770	98,405,544	95.84%
HET-H3K4me3	83,648,876	80,038,106	95.68%
WT-HA	80,456,177	77,476,943	96.30%
HET-HA	80,002,694	76,867,740	96.08%

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.

Sample	Total reads	Aligned reads	Concordant alignment rate	Bowtie2 report
WT-H3K27ac-1	35,377,936	25,405,636	71.81%	bam.bowtie/WT-H3K27ac-1.bt2stats.html
WT-H3K27ac-2	38,001,608	26,508,659	69.76%	bam.bowtie/WT-H3K27ac-2.bt2stats.html
WT-H3K27ac-3	36,493,684	26,392,881	72.32%	bam.bowtie/WT-H3K27ac-3.bt2stats.html
WT-IgG-1	36,719,558	18,174,936	49.50%	bam.bowtie/WT-IgG-1.bt2stats.html
WT-IgG-2	37,426,036	20,290,788	54.22%	bam.bowtie/WT-IgG-2.bt2stats.html
WT-IgG-3	35,294,530	15,895,198	45.04%	bam.bowtie/WT-IgG-3.bt2stats.html
HET-H3K27ac-1	28,184,664	20,071,962	71.22%	bam.bowtie/HET-H3K27ac-1.bt2stats.html
HET-H3K27ac-2	28,984,481	17,079,790	58.93%	bam.bowtie/HET-H3K27ac-2.bt2stats.html
HET-H3K27ac-3	33,031,969	19,044,831	57.66%	bam.bowtie/HET-H3K27ac-3.bt2stats.html
HET-IgG-1	33,316,847	13,463,902	40.41%	bam.bowtie/HET-IgG-1.bt2stats.html
HET-IgG-2	35,073,720	16,094,598	45.89%	bam.bowtie/HET-IgG-2.bt2stats.html
HET-IgG-3	37,136,094	17,554,027	47.27%	bam.bowtie/HET-IgG-3.bt2stats.html
WT-H3K27me3-1	36,834,262	26,781,293	72.71%	bam.bowtie/WT-H3K27me3-1.bt2stats.html
WT-H3K27me3-2	38,716,112	29,735,433	76.80%	bam.bowtie/WT-H3K27me3-2.bt2stats.html
WT-H3K27me3-3	38,381,932	29,153,392	75.96%	bam.bowtie/WT-H3K27me3-3.bt2stats.html
HET-H3K27me3-1	32,028,139	23,607,903	73.71%	bam.bowtie/HET-H3K27me3-1.bt2stats.html
HET-H3K27me3-2	38,568,107	28,772,387	74.60%	bam.bowtie/HET-H3K27me3-2.bt2stats.html
HET-H3K27me3-3	32,694,911	24,630,269	75.33%	bam.bowtie/HET-H3K27me3-3.bt2stats.html
WT-H3K4me3-1	33,597,231	21,747,366	64.73%	bam.bowtie/WT-H3K4me3-1.bt2stats.html
WT-H3K4me3-2	30,586,567	19,226,315	62.86%	bam.bowtie/WT-H3K4me3-2.bt2stats.html
WT-H3K4me3-3	34,221,746	22,778,963	66.56%	bam.bowtie/WT-H3K4me3-3.bt2stats.html
HET-H3K4me3-1	25,557,181	15,405,482	60.28%	bam.bowtie/HET-H3K4me3-1.bt2stats.html
HET-H3K4me3-2	29,651,098	18,811,132	63.44%	bam.bowtie/HET-H3K4me3-2.bt2stats.html
HET-H3K4me3-3	24,829,827	16,114,824	64.90%	bam.bowtie/HET-H3K4me3-3.bt2stats.html
WT-HA-1	37,462,024	18,726,622	49.99%	bam.bowtie/WT-HA-1.bt2stats.html
WT-HA-2	40,014,919	21,467,252	53.65%	bam.bowtie/WT-HA-2.bt2stats.html
HET-HA-1	37,719,703	21,957,077	58.21%	bam.bowtie/HET-HA-1.bt2stats.html
HET-HA-2	39,148,037	22,802,872	58.25%	bam.bowtie/HET-HA-2.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.

Name	Total nt	Coverage	Effective bp	Effective Perc	Eff Coverage
WT-H3K27ac-1	3,122,782,725	1.01	310,692,217	10.10%	10.05
WT-H3K27ac-2	3,491,995,063	1.13	340,396,825	11.00%	10.26
WT-H3K27ac-3	3,370,444,023	1.09	330,045,257	10.70%	10.21
WT-IgG-1	704,316,356	0.23	82,046,240	2.70%	8.58
WT-IgG-2	630,071,920	0.20	70,751,582	2.30%	8.91
WT-IgG-3	811,531,521	0.26	95,749,924	3.10%	8.48
HET-H3K27ac-1	1,288,150,468	0.42	148,589,931	4.80%	8.67
HET-H3K27ac-2	1,651,104,087	0.53	176,250,800	5.70%	9.37
HET-H3K27ac-3	2,078,943,274	0.67	237,539,430	7.70%	8.75
HET-IgG-1	561,815,932	0.18	64,935,514	2.10%	8.65
HET-IgG-2	685,975,728	0.22	81,028,032	2.60%	8.47
HET-IgG-3	808,261,669	0.26	96,083,824	3.10%	8.41
WT-H3K27me3-1	4,682,444,375	1.52	364,790,459	11.80%	12.84
WT-H3K27me3-2	4,980,357,262	1.61	415,818,700	13.50%	11.98
WT-H3K27me3-3	5,197,628,818	1.68	417,070,989	13.50%	12.46
HET-H3K27me3-1	4,241,209,445	1.37	323,222,669	10.50%	13.12
HET-H3K27me3-2	5,566,480,302	1.80	386,797,697	12.50%	14.39
HET-H3K27me3-3	4,228,893,851	1.37	329,550,963	10.70%	12.83
WT-H3K4me3-1	3,300,282,673	1.07	39,322,295	1.30%	83.93
WT-H3K4me3-2	3,056,001,609	0.99	37,896,834	1.20%	80.64
WT-H3K4me3-3	3,500,300,263	1.13	42,247,118	1.40%	82.85
HET-H3K4me3-1	2,454,726,064	0.80	36,597,203	1.20%	67.07
HET-H3K4me3-2	2,836,948,824	0.92	37,077,290	1.20%	76.51
HET-H3K4me3-3	2,698,791,263	0.87	34,970,271	1.10%	77.17
WT-HA-1	1,849,058,225	0.60	229,556,179	7.40%	8.05
WT-HA-2	2,433,211,469	0.79	298,753,987	9.70%	8.14
HET-HA-1	2,635,242,751	0.85	306,128,692	9.90%	8.61
HET-HA-2	2,615,512,910	0.85	301,528,200	9.80%	8.67

Table 7. Genome coverage by sample.

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

Name	Total nt	Coverage	Effective bp	Effective Perc	Eff Coverage
WT-H3K27ac	17,275,115,714	5.60	1,279,151,810	41.40%	13.51
HET-H3K27ac	10,883,117,798	3.53	1,002,589,714	32.50%	10.86
WT-H3K27me3	0	0.00	0	0.00%	0.00
HET-H3K27me3	17,991,793,142	5.83	845,073,368	27.40%	21.29
WT-H3K4me3	10,322,974,375	3.34	107,778,507	3.50%	95.78
HET-H3K4me3	8,362,056,214	2.71	89,945,153	2.90%	92.97
WT-HA	7,824,094,683	2.53	826,823,940	26.80%	9.46
HET-HA	8,823,167,425	2.86	867,209,072	28.10%	10.17

Table 8. Genome coverage by condition

File: H2B_CR_20230613.sample.cov.xlsx
Size: 67.70 kB
Description: Per-chromosome coverage data, by sample.

File: H2B_CR_20230613.cond.cov.xlsx
Size: 21.26 kB
Description: Per-chromosome coverage data, by condition.

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

Condition	Total Peaks	Peaks	Actions
WT-H3K27ac	3,074	WT-H3K27ac.peaks.bed	Create RegionSet
HET-H3K27ac	1,348	HET-H3K27ac.peaks.bed	Create RegionSet
WT-H3K27me3	3,855	WT-H3K27me3.peaks.bed	Create RegionSet
HET-H3K27me3	4,067	HET-H3K27me3.peaks.bed	Create RegionSet
WT-H3K4me3	5,589	WT-H3K4me3.peaks.bed	Create RegionSet
HET-H3K4me3	5,712	HET-H3K4me3.peaks.bed	Create RegionSet
WT-HA	142,414	WT-HA.peaks.bed	Create RegionSet
HET-HA	142,409	HET-HA.peaks.bed	Create RegionSet

Table 9. 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: 5.85 kB
Description: Table containing number of peaks in each region for each condition.

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.

Condition	Reads	Reads in peaks	FRIP
WT-H3K27ac	195,726,962	14,152,239	7.23%
HET-H3K27ac	147,350,982	3,486,114	2.37%
WT-H3K27me3	209,812,287	36,791,307	17.54%
HET-H3K27me3	191,028,475	39,758,661	20.81%
WT-H3K4me3	149,619,382	92,692,120	61.95%
HET-H3K4me3	118,861,012	73,575,110	61.90%
WT-HA	112,921,897	22,545,702	19.97%
HET-HA	122,034,153	29,871,163	24.48%

Table 10. Fraction of Reads in Peaks

7. 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.

Test	Control	Total	Increased	Decreased	Unchanged	Table
HET-H3K27ac	WT-H3K27ac	1,306	0%	74%	24%	HET-H3K27ac.vs.WT-H3K27ac.xlsx
HET-H3K27me3	WT-H3K27me3	3,385	17%	23%	59%	HET-H3K27me3.vs.WT-H3K27me3.xlsx
HET-H3K4me3	WT-H3K4me3	5,452	0%	9%	89%	HET-H3K4me3.vs.WT-H3K4me3.xlsx
HET-HA	WT-HA	95,569	47%	19%	32%	HET-HA.vs.WT-HA.xlsx

Show values | percentages
Table 11. Differential peak analysis results.

8. 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

9. UCSC hub

UCSC Genome Browser: use the previous link to display the data tracks automatically, or copy the the URL https://lichtlab.cancer.ufl.edu/reports/H2B//H2B_CR_20230613/H2B_CR_20230613/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://lichtlab.cancer.ufl.edu/reports/H2B//H2B_CR_20230613/H2B_CR_20230613/hub.json.

Completed: 6-20-2023@23:20