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ChIPseq - Alignment and peak finding

Title: NSD2_CS_RCHACV_070218_Mohammad
Project: https://basespace.illumina.com/run/96022930/UTX_CS_ARP_HA_KARPAS_061218_DAPHNE
Started on: 8/29/2018 11:00:27
Hostname: login1.ufhpc
Run directory: /ufrc/riva/ariva/collab/licht/runs/NSD2-E1099K-Project/NSD2_CS_RCHACV_070218_Mohammad/NSD2_CS_RCHACV_070218_Mohammad
Configuration chipseq.conf

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*
Contrasts:	2C-EZH2 vs. 9B-EZH2, 2C-H2AK119ub vs. 9B-H2AK119ub, 2C-H3K27ac vs. 9B-H3K27ac, 2C-H3K27me3 vs. 9B-H3K27me3, 2C-H3K36me2 vs. 9B-H3K36me2, 2C-NSD2 vs. 9B-NSD2
Conditions:	2C-EZH2, 2C-H2AK119ub, 2C-H3K27ac, 2C-H3K27me3, 2C-H3K36me2, 2C-NSD2, 9B-EZH2, 9B-H2AK119ub, 9B-H3K27ac, 9B-H3K27me3, 9B-H3K36me2, 9B-NSD2
2C-EZH2	RCHACV-2C-EZH2 (4 readsets)
2C-H2AK119ub	RCHACV-2C-H2AK119ub (4 readsets)
2C-H3K27ac	RCHACV-2C-H3K27ac (4 readsets)
2C-H3K27me3	RCHACV-2C-H3K27me3 (4 readsets)
2C-H3K36me2	RCHACV-2C-H3K36me2 (4 readsets)
2C-NSD2	RCHACV-2C-NSD2 (4 readsets)
9B-EZH2	RCHACV-9B-EZH2 (4 readsets)
9B-H2AK119ub	RCHACV-9B-H2AK119ub (4 readsets)
9B-H3K27ac	RCHACV-9B-H3K27ac (4 readsets)
9B-H3K27me3	RCHACV-9B-H3K27me3 (4 readsets)
9B-H3K36me2	RCHACV-9B-H3K36me2 (4 readsets)
9B-NSD2	RCHACV-9B-NSD2 (4 readsets)

Table 1. Summary of input data

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
RCHACV-2C-EZH2	RCHACV-2C-EZH2_r1	11,686,727	RCHACV-2C-EZH2_S0_L001_R1_001 RCHACV-2C-EZH2_S0_L001_R2_001	11,116,569	RCHACV-2C-EZH2_S0_L001_R1_001.trim.paired RCHACV-2C-EZH2_S0_L001_R2_001.trim.paired	95.12%
	RCHACV-2C-EZH2_r2	11,983,230	RCHACV-2C-EZH2_S0_L002_R1_001 RCHACV-2C-EZH2_S0_L002_R2_001	11,385,306	RCHACV-2C-EZH2_S0_L002_R1_001.trim.paired RCHACV-2C-EZH2_S0_L002_R2_001.trim.paired	95.01%
	RCHACV-2C-EZH2_r3	11,642,324	RCHACV-2C-EZH2_S0_L003_R1_001 RCHACV-2C-EZH2_S0_L003_R2_001	11,127,542	RCHACV-2C-EZH2_S0_L003_R1_001.trim.paired RCHACV-2C-EZH2_S0_L003_R2_001.trim.paired	95.58%
	RCHACV-2C-EZH2_r4	12,066,534	RCHACV-2C-EZH2_S0_L004_R1_001 RCHACV-2C-EZH2_S0_L004_R2_001	11,462,389	RCHACV-2C-EZH2_S0_L004_R1_001.trim.paired RCHACV-2C-EZH2_S0_L004_R2_001.trim.paired	94.99%
RCHACV-2C-H2AK119ub	RCHACV-2C-H2AK119ub_r1	11,129,932	RCHACV-2C-H2AK119ub_S0_L001_R1_001 RCHACV-2C-H2AK119ub_S0_L001_R2_001	10,589,134	RCHACV-2C-H2AK119ub_S0_L001_R1_001.trim.paired RCHACV-2C-H2AK119ub_S0_L001_R2_001.trim.paired	95.14%
	RCHACV-2C-H2AK119ub_r2	11,449,589	RCHACV-2C-H2AK119ub_S0_L002_R1_001 RCHACV-2C-H2AK119ub_S0_L002_R2_001	10,887,687	RCHACV-2C-H2AK119ub_S0_L002_R1_001.trim.paired RCHACV-2C-H2AK119ub_S0_L002_R2_001.trim.paired	95.09%
	RCHACV-2C-H2AK119ub_r3	11,102,220	RCHACV-2C-H2AK119ub_S0_L003_R1_001 RCHACV-2C-H2AK119ub_S0_L003_R2_001	10,617,877	RCHACV-2C-H2AK119ub_S0_L003_R1_001.trim.paired RCHACV-2C-H2AK119ub_S0_L003_R2_001.trim.paired	95.64%
	RCHACV-2C-H2AK119ub_r4	11,556,088	RCHACV-2C-H2AK119ub_S0_L004_R1_001 RCHACV-2C-H2AK119ub_S0_L004_R2_001	10,981,933	RCHACV-2C-H2AK119ub_S0_L004_R1_001.trim.paired RCHACV-2C-H2AK119ub_S0_L004_R2_001.trim.paired	95.03%
RCHACV-2C-H3K27ac	RCHACV-2C-H3K27ac_r1	7,474,397	RCHACV-2C-H3K27ac_S0_L001_R1_001 RCHACV-2C-H3K27ac_S0_L001_R2_001	7,140,689	RCHACV-2C-H3K27ac_S0_L001_R1_001.trim.paired RCHACV-2C-H3K27ac_S0_L001_R2_001.trim.paired	95.54%
	RCHACV-2C-H3K27ac_r2	7,633,201	RCHACV-2C-H3K27ac_S0_L002_R1_001 RCHACV-2C-H3K27ac_S0_L002_R2_001	7,288,641	RCHACV-2C-H3K27ac_S0_L002_R1_001.trim.paired RCHACV-2C-H3K27ac_S0_L002_R2_001.trim.paired	95.49%
	RCHACV-2C-H3K27ac_r3	7,423,877	RCHACV-2C-H3K27ac_S0_L003_R1_001 RCHACV-2C-H3K27ac_S0_L003_R2_001	7,123,365	RCHACV-2C-H3K27ac_S0_L003_R1_001.trim.paired RCHACV-2C-H3K27ac_S0_L003_R2_001.trim.paired	95.95%
	RCHACV-2C-H3K27ac_r4	7,666,536	RCHACV-2C-H3K27ac_S0_L004_R1_001 RCHACV-2C-H3K27ac_S0_L004_R2_001	7,320,015	RCHACV-2C-H3K27ac_S0_L004_R1_001.trim.paired RCHACV-2C-H3K27ac_S0_L004_R2_001.trim.paired	95.48%
RCHACV-2C-H3K27me3	RCHACV-2C-H3K27me3_r1	10,073,957	RCHACV-2C-H3K27me3_S0_L001_R1_001 RCHACV-2C-H3K27me3_S0_L001_R2_001	9,604,658	RCHACV-2C-H3K27me3_S0_L001_R1_001.trim.paired RCHACV-2C-H3K27me3_S0_L001_R2_001.trim.paired	95.34%
	RCHACV-2C-H3K27me3_r2	10,302,342	RCHACV-2C-H3K27me3_S0_L002_R1_001 RCHACV-2C-H3K27me3_S0_L002_R2_001	9,814,367	RCHACV-2C-H3K27me3_S0_L002_R1_001.trim.paired RCHACV-2C-H3K27me3_S0_L002_R2_001.trim.paired	95.26%
	RCHACV-2C-H3K27me3_r3	10,013,431	RCHACV-2C-H3K27me3_S0_L003_R1_001 RCHACV-2C-H3K27me3_S0_L003_R2_001	9,590,492	RCHACV-2C-H3K27me3_S0_L003_R1_001.trim.paired RCHACV-2C-H3K27me3_S0_L003_R2_001.trim.paired	95.78%
	RCHACV-2C-H3K27me3_r4	10,455,813	RCHACV-2C-H3K27me3_S0_L004_R1_001 RCHACV-2C-H3K27me3_S0_L004_R2_001	9,946,969	RCHACV-2C-H3K27me3_S0_L004_R1_001.trim.paired RCHACV-2C-H3K27me3_S0_L004_R2_001.trim.paired	95.13%
RCHACV-2C-H3K36me2	RCHACV-2C-H3K36me2_r1	7,765,767	RCHACV-2C-H3K36me2_S0_L001_R1_001 RCHACV-2C-H3K36me2_S0_L001_R2_001	7,414,115	RCHACV-2C-H3K36me2_S0_L001_R1_001.trim.paired RCHACV-2C-H3K36me2_S0_L001_R2_001.trim.paired	95.47%
	RCHACV-2C-H3K36me2_r2	7,979,659	RCHACV-2C-H3K36me2_S0_L002_R1_001 RCHACV-2C-H3K36me2_S0_L002_R2_001	7,618,550	RCHACV-2C-H3K36me2_S0_L002_R1_001.trim.paired RCHACV-2C-H3K36me2_S0_L002_R2_001.trim.paired	95.47%
	RCHACV-2C-H3K36me2_r3	7,727,634	RCHACV-2C-H3K36me2_S0_L003_R1_001 RCHACV-2C-H3K36me2_S0_L003_R2_001	7,410,445	RCHACV-2C-H3K36me2_S0_L003_R1_001.trim.paired RCHACV-2C-H3K36me2_S0_L003_R2_001.trim.paired	95.90%
	RCHACV-2C-H3K36me2_r4	8,046,533	RCHACV-2C-H3K36me2_S0_L004_R1_001 RCHACV-2C-H3K36me2_S0_L004_R2_001	7,677,944	RCHACV-2C-H3K36me2_S0_L004_R1_001.trim.paired RCHACV-2C-H3K36me2_S0_L004_R2_001.trim.paired	95.42%
RCHACV-2C-NSD2	RCHACV-2C-NSD2_r1	8,947,748	RCHACV-2C-NSD2_S0_L001_R1_001 RCHACV-2C-NSD2_S0_L001_R2_001	8,544,109	RCHACV-2C-NSD2_S0_L001_R1_001.trim.paired RCHACV-2C-NSD2_S0_L001_R2_001.trim.paired	95.49%
	RCHACV-2C-NSD2_r2	9,107,494	RCHACV-2C-NSD2_S0_L002_R1_001 RCHACV-2C-NSD2_S0_L002_R2_001	8,705,655	RCHACV-2C-NSD2_S0_L002_R1_001.trim.paired RCHACV-2C-NSD2_S0_L002_R2_001.trim.paired	95.59%
	RCHACV-2C-NSD2_r3	8,891,732	RCHACV-2C-NSD2_S0_L003_R1_001 RCHACV-2C-NSD2_S0_L003_R2_001	8,532,075	RCHACV-2C-NSD2_S0_L003_R1_001.trim.paired RCHACV-2C-NSD2_S0_L003_R2_001.trim.paired	95.96%
	RCHACV-2C-NSD2_r4	9,143,621	RCHACV-2C-NSD2_S0_L004_R1_001 RCHACV-2C-NSD2_S0_L004_R2_001	8,735,662	RCHACV-2C-NSD2_S0_L004_R1_001.trim.paired RCHACV-2C-NSD2_S0_L004_R2_001.trim.paired	95.54%
RCHACV-9B-EZH2	RCHACV-9B-EZH2_r1	7,150,569	RCHACV-9B-EZH2_S0_L001_R1_001 RCHACV-9B-EZH2_S0_L001_R2_001	6,795,885	RCHACV-9B-EZH2_S0_L001_R1_001.trim.paired RCHACV-9B-EZH2_S0_L001_R2_001.trim.paired	95.04%
	RCHACV-9B-EZH2_r2	7,346,761	RCHACV-9B-EZH2_S0_L002_R1_001 RCHACV-9B-EZH2_S0_L002_R2_001	6,988,604	RCHACV-9B-EZH2_S0_L002_R1_001.trim.paired RCHACV-9B-EZH2_S0_L002_R2_001.trim.paired	95.12%
	RCHACV-9B-EZH2_r3	7,145,735	RCHACV-9B-EZH2_S0_L003_R1_001 RCHACV-9B-EZH2_S0_L003_R2_001	6,825,728	RCHACV-9B-EZH2_S0_L003_R1_001.trim.paired RCHACV-9B-EZH2_S0_L003_R2_001.trim.paired	95.52%
	RCHACV-9B-EZH2_r4	7,372,435	RCHACV-9B-EZH2_S0_L004_R1_001 RCHACV-9B-EZH2_S0_L004_R2_001	7,011,792	RCHACV-9B-EZH2_S0_L004_R1_001.trim.paired RCHACV-9B-EZH2_S0_L004_R2_001.trim.paired	95.11%
RCHACV-9B-H2AK119ub	RCHACV-9B-H2AK119ub_r1	10,761,036	RCHACV-9B-H2AK119ub_S0_L001_R1_001 RCHACV-9B-H2AK119ub_S0_L001_R2_001	10,179,322	RCHACV-9B-H2AK119ub_S0_L001_R1_001.trim.paired RCHACV-9B-H2AK119ub_S0_L001_R2_001.trim.paired	94.59%
	RCHACV-9B-H2AK119ub_r2	11,162,986	RCHACV-9B-H2AK119ub_S0_L002_R1_001 RCHACV-9B-H2AK119ub_S0_L002_R2_001	10,558,232	RCHACV-9B-H2AK119ub_S0_L002_R1_001.trim.paired RCHACV-9B-H2AK119ub_S0_L002_R2_001.trim.paired	94.58%
	RCHACV-9B-H2AK119ub_r3	10,791,781	RCHACV-9B-H2AK119ub_S0_L003_R1_001 RCHACV-9B-H2AK119ub_S0_L003_R2_001	10,266,409	RCHACV-9B-H2AK119ub_S0_L003_R1_001.trim.paired RCHACV-9B-H2AK119ub_S0_L003_R2_001.trim.paired	95.13%
	RCHACV-9B-H2AK119ub_r4	11,250,736	RCHACV-9B-H2AK119ub_S0_L004_R1_001 RCHACV-9B-H2AK119ub_S0_L004_R2_001	10,625,105	RCHACV-9B-H2AK119ub_S0_L004_R1_001.trim.paired RCHACV-9B-H2AK119ub_S0_L004_R2_001.trim.paired	94.44%
RCHACV-9B-H3K27ac	RCHACV-9B-H3K27ac_r1	8,010,614	RCHACV-9B-H3K27ac_S0_L001_R1_001 RCHACV-9B-H3K27ac_S0_L001_R2_001	7,654,929	RCHACV-9B-H3K27ac_S0_L001_R1_001.trim.paired RCHACV-9B-H3K27ac_S0_L001_R2_001.trim.paired	95.56%
	RCHACV-9B-H3K27ac_r2	8,166,314	RCHACV-9B-H3K27ac_S0_L002_R1_001 RCHACV-9B-H3K27ac_S0_L002_R2_001	7,789,946	RCHACV-9B-H3K27ac_S0_L002_R1_001.trim.paired RCHACV-9B-H3K27ac_S0_L002_R2_001.trim.paired	95.39%
	RCHACV-9B-H3K27ac_r3	7,950,796	RCHACV-9B-H3K27ac_S0_L003_R1_001 RCHACV-9B-H3K27ac_S0_L003_R2_001	7,626,533	RCHACV-9B-H3K27ac_S0_L003_R1_001.trim.paired RCHACV-9B-H3K27ac_S0_L003_R2_001.trim.paired	95.92%
	RCHACV-9B-H3K27ac_r4	8,248,803	RCHACV-9B-H3K27ac_S0_L004_R1_001 RCHACV-9B-H3K27ac_S0_L004_R2_001	7,869,517	RCHACV-9B-H3K27ac_S0_L004_R1_001.trim.paired RCHACV-9B-H3K27ac_S0_L004_R2_001.trim.paired	95.40%
RCHACV-9B-H3K27me3	RCHACV-9B-H3K27me3_r1	8,787,859	RCHACV-9B-H3K27me3_S0_L001_R1_001 RCHACV-9B-H3K27me3_S0_L001_R2_001	8,357,344	RCHACV-9B-H3K27me3_S0_L001_R1_001.trim.paired RCHACV-9B-H3K27me3_S0_L001_R2_001.trim.paired	95.10%
	RCHACV-9B-H3K27me3_r2	8,750,966	RCHACV-9B-H3K27me3_S0_L002_R1_001 RCHACV-9B-H3K27me3_S0_L002_R2_001	8,306,023	RCHACV-9B-H3K27me3_S0_L002_R1_001.trim.paired RCHACV-9B-H3K27me3_S0_L002_R2_001.trim.paired	94.92%
	RCHACV-9B-H3K27me3_r3	8,519,822	RCHACV-9B-H3K27me3_S0_L003_R1_001 RCHACV-9B-H3K27me3_S0_L003_R2_001	8,136,672	RCHACV-9B-H3K27me3_S0_L003_R1_001.trim.paired RCHACV-9B-H3K27me3_S0_L003_R2_001.trim.paired	95.50%
	RCHACV-9B-H3K27me3_r4	8,850,690	RCHACV-9B-H3K27me3_S0_L004_R1_001 RCHACV-9B-H3K27me3_S0_L004_R2_001	8,399,248	RCHACV-9B-H3K27me3_S0_L004_R1_001.trim.paired RCHACV-9B-H3K27me3_S0_L004_R2_001.trim.paired	94.90%
RCHACV-9B-H3K36me2	RCHACV-9B-H3K36me2_r1	6,959,779	RCHACV-9B-H3K36me2_S0_L001_R1_001 RCHACV-9B-H3K36me2_S0_L001_R2_001	6,616,531	RCHACV-9B-H3K36me2_S0_L001_R1_001.trim.paired RCHACV-9B-H3K36me2_S0_L001_R2_001.trim.paired	95.07%
	RCHACV-9B-H3K36me2_r2	7,159,359	RCHACV-9B-H3K36me2_S0_L002_R1_001 RCHACV-9B-H3K36me2_S0_L002_R2_001	6,803,214	RCHACV-9B-H3K36me2_S0_L002_R1_001.trim.paired RCHACV-9B-H3K36me2_S0_L002_R2_001.trim.paired	95.03%
	RCHACV-9B-H3K36me2_r3	6,954,174	RCHACV-9B-H3K36me2_S0_L003_R1_001 RCHACV-9B-H3K36me2_S0_L003_R2_001	6,644,734	RCHACV-9B-H3K36me2_S0_L003_R1_001.trim.paired RCHACV-9B-H3K36me2_S0_L003_R2_001.trim.paired	95.55%
	RCHACV-9B-H3K36me2_r4	7,213,391	RCHACV-9B-H3K36me2_S0_L004_R1_001 RCHACV-9B-H3K36me2_S0_L004_R2_001	6,850,475	RCHACV-9B-H3K36me2_S0_L004_R1_001.trim.paired RCHACV-9B-H3K36me2_S0_L004_R2_001.trim.paired	94.97%
RCHACV-9B-NSD2	RCHACV-9B-NSD2_r1	9,390,114	RCHACV-9B-NSD2_S0_L001_R1_001 RCHACV-9B-NSD2_S0_L001_R2_001	8,977,382	RCHACV-9B-NSD2_S0_L001_R1_001.trim.paired RCHACV-9B-NSD2_S0_L001_R2_001.trim.paired	95.60%
	RCHACV-9B-NSD2_r2	9,533,900	RCHACV-9B-NSD2_S0_L002_R1_001 RCHACV-9B-NSD2_S0_L002_R2_001	9,109,524	RCHACV-9B-NSD2_S0_L002_R1_001.trim.paired RCHACV-9B-NSD2_S0_L002_R2_001.trim.paired	95.55%
	RCHACV-9B-NSD2_r3	9,328,941	RCHACV-9B-NSD2_S0_L003_R1_001 RCHACV-9B-NSD2_S0_L003_R2_001	8,958,012	RCHACV-9B-NSD2_S0_L003_R1_001.trim.paired RCHACV-9B-NSD2_S0_L003_R2_001.trim.paired	96.02%
	RCHACV-9B-NSD2_r4	9,602,825	RCHACV-9B-NSD2_S0_L004_R1_001 RCHACV-9B-NSD2_S0_L004_R2_001	9,173,005	RCHACV-9B-NSD2_S0_L004_R1_001.trim.paired RCHACV-9B-NSD2_S0_L004_R2_001.trim.paired	95.52%

Table 2. 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
RCHACV-2C-EZH2	47,378,815	45,091,806	95.17%
RCHACV-2C-H2AK119ub	45,237,829	43,076,631	95.22%
RCHACV-2C-H3K27ac	30,198,011	28,872,710	95.61%
RCHACV-2C-H3K27me3	40,845,543	38,956,486	95.38%
RCHACV-2C-H3K36me2	31,519,593	30,121,054	95.56%
RCHACV-2C-NSD2	36,090,595	34,517,501	95.64%
RCHACV-9B-EZH2	29,015,500	27,622,009	95.20%
RCHACV-9B-H2AK119ub	43,966,539	41,629,068	94.68%
RCHACV-9B-H3K27ac	32,376,527	30,940,925	95.57%
RCHACV-9B-H3K27me3	34,909,337	33,199,287	95.10%
RCHACV-9B-H3K36me2	28,286,703	26,914,954	95.15%
RCHACV-9B-NSD2	37,855,780	36,217,923	95.67%

Table 3. Number of reads in each sample before and after QC.

Condition	Reads before QC	Reads after QC	% Retained
2C-EZH2	47,378,815	45,091,806	95.17%
2C-H2AK119ub	45,237,829	43,076,631	95.22%
2C-H3K27ac	30,198,011	28,872,710	95.61%
2C-H3K27me3	40,845,543	38,956,486	95.38%
2C-H3K36me2	31,519,593	30,121,054	95.56%
2C-NSD2	36,090,595	34,517,501	95.64%
9B-EZH2	29,015,500	27,622,009	95.20%
9B-H2AK119ub	43,966,539	41,629,068	94.68%
9B-H3K27ac	32,376,527	30,940,925	95.57%
9B-H3K27me3	34,909,337	33,199,287	95.10%
9B-H3K36me2	28,286,703	26,914,954	95.15%
9B-NSD2	37,855,780	36,217,923	95.67%

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

3. Alignment to genome
The input sequences were aligned to the genome using Bowtie 2.3.4.2. 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.

Sample	Total reads	Aligned reads	Concordant alignment rate	Bowtie2 report
RCHACV-2C-EZH2	45,091,806	24,226,981	53.73%	RCHACV-2C-EZH2.bt2stats.html
RCHACV-2C-H2AK119ub	43,076,631	23,731,978	55.09%	RCHACV-2C-H2AK119ub.bt2stats.html
RCHACV-2C-H3K27ac	28,872,710	14,393,761	49.85%	RCHACV-2C-H3K27ac.bt2stats.html
RCHACV-2C-H3K27me3	38,956,486	17,256,953	44.30%	RCHACV-2C-H3K27me3.bt2stats.html
RCHACV-2C-H3K36me2	30,121,054	16,659,398	55.31%	RCHACV-2C-H3K36me2.bt2stats.html
RCHACV-2C-NSD2	34,517,501	18,784,999	54.42%	RCHACV-2C-NSD2.bt2stats.html
RCHACV-9B-EZH2	27,622,009	16,167,070	58.53%	RCHACV-9B-EZH2.bt2stats.html
RCHACV-9B-H2AK119ub	41,629,068	28,199,830	67.74%	RCHACV-9B-H2AK119ub.bt2stats.html
RCHACV-9B-H3K27ac	30,940,925	12,105,506	39.12%	RCHACV-9B-H3K27ac.bt2stats.html
RCHACV-9B-H3K27me3	33,199,287	10,739,477	32.35%	RCHACV-9B-H3K27me3.bt2stats.html
RCHACV-9B-H3K36me2	26,914,954	16,013,113	59.50%	RCHACV-9B-H3K36me2.bt2stats.html
RCHACV-9B-NSD2	36,217,923	15,329,195	42.32%	RCHACV-9B-NSD2.bt2stats.html

Table 5. 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
RCHACV-2C-EZH2	298,967,215	0.10	28,902,044	0.90%	10.34
RCHACV-2C-H2AK119ub	477,661,587	0.15	57,666,514	1.90%	8.28
RCHACV-2C-H3K27ac	261,058,624	0.08	28,331,580	0.90%	9.21
RCHACV-2C-H3K27me3	424,097,581	0.14	30,447,492	1.00%	13.93
RCHACV-2C-H3K36me2	196,419,731	0.06	22,256,229	0.70%	8.83
RCHACV-2C-NSD2	263,725,074	0.09	29,353,851	1.00%	8.98
RCHACV-9B-EZH2	195,978,777	0.06	18,599,924	0.60%	10.54
RCHACV-9B-H2AK119ub	585,385,277	0.19	71,836,445	2.30%	8.15
RCHACV-9B-H3K27ac	199,797,478	0.06	21,796,507	0.70%	9.17
RCHACV-9B-H3K27me3	372,071,480	0.12	19,437,135	0.60%	19.14
RCHACV-9B-H3K36me2	140,910,284	0.05	14,832,651	0.50%	9.50
RCHACV-9B-NSD2	175,585,536	0.06	18,894,654	0.60%	9.29

Table 6. 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
2C-EZH2	298,967,215	0.10	28,902,044	0.90%	10.34
2C-H2AK119ub	477,661,587	0.15	57,666,514	1.90%	8.28
2C-H3K27ac	261,058,624	0.08	28,331,580	0.90%	9.21
2C-H3K27me3	424,097,581	0.14	30,447,492	1.00%	13.93
2C-H3K36me2	196,419,731	0.06	22,256,229	0.70%	8.83
2C-NSD2	263,725,074	0.09	29,353,851	1.00%	8.98
9B-EZH2	195,978,777	0.06	18,599,924	0.60%	10.54
9B-H2AK119ub	585,385,277	0.19	71,836,445	2.30%	8.15
9B-H3K27ac	199,797,478	0.06	21,796,507	0.70%	9.17
9B-H3K27me3	372,071,480	0.12	19,437,135	0.60%	19.14
9B-H3K36me2	140,910,284	0.05	14,832,651	0.50%	9.50
9B-NSD2	175,585,536	0.06	18,894,654	0.60%	9.29

Table 7. Genome coverage by condition

File: NSD2_CS_RCHACV_070218_Mohammad.sample.cov.xlsx
Size: 30.20 kB
Description: Per-chromosome coverage data, by sample.

File: NSD2_CS_RCHACV_070218_Mohammad.cond.cov.xlsx
Size: 30.18 kB
Description: Per-chromosome coverage data, by condition.

5. Peak detection
Peak detection was performed using MACS version 2.1.1.20160309. The following table provides links to the Pileup, narrowPeaks, and Summits files for each condition. All files are in bedGraph format.

Condition	Pileup	Peaks	Summits
2C-EZH2	2C-EZH2.macs/2C-EZH2.bedGraph	2C-EZH2.macs/2C-EZH2.npeaks.bedGraph	2C-EZH2.macs/2C-EZH2.summits.bedGraph
2C-H2AK119ub	2C-H2AK119ub.macs/2C-H2AK119ub.bedGraph	2C-H2AK119ub.macs/2C-H2AK119ub.npeaks.bedGraph	2C-H2AK119ub.macs/2C-H2AK119ub.summits.bedGraph
2C-H3K27ac	2C-H3K27ac.macs/2C-H3K27ac.bedGraph	2C-H3K27ac.macs/2C-H3K27ac.npeaks.bedGraph	2C-H3K27ac.macs/2C-H3K27ac.summits.bedGraph
2C-H3K27me3	2C-H3K27me3.macs/2C-H3K27me3.bedGraph	2C-H3K27me3.macs/2C-H3K27me3.npeaks.bedGraph	2C-H3K27me3.macs/2C-H3K27me3.summits.bedGraph
2C-H3K36me2	2C-H3K36me2.macs/2C-H3K36me2.bedGraph	2C-H3K36me2.macs/2C-H3K36me2.npeaks.bedGraph	2C-H3K36me2.macs/2C-H3K36me2.summits.bedGraph
2C-NSD2	2C-NSD2.macs/2C-NSD2.bedGraph	2C-NSD2.macs/2C-NSD2.npeaks.bedGraph	2C-NSD2.macs/2C-NSD2.summits.bedGraph
9B-EZH2	9B-EZH2.macs/9B-EZH2.bedGraph	9B-EZH2.macs/9B-EZH2.npeaks.bedGraph	9B-EZH2.macs/9B-EZH2.summits.bedGraph
9B-H2AK119ub	9B-H2AK119ub.macs/9B-H2AK119ub.bedGraph	9B-H2AK119ub.macs/9B-H2AK119ub.npeaks.bedGraph	9B-H2AK119ub.macs/9B-H2AK119ub.summits.bedGraph
9B-H3K27ac	9B-H3K27ac.macs/9B-H3K27ac.bedGraph	9B-H3K27ac.macs/9B-H3K27ac.npeaks.bedGraph	9B-H3K27ac.macs/9B-H3K27ac.summits.bedGraph
9B-H3K27me3	9B-H3K27me3.macs/9B-H3K27me3.bedGraph	9B-H3K27me3.macs/9B-H3K27me3.npeaks.bedGraph	9B-H3K27me3.macs/9B-H3K27me3.summits.bedGraph
9B-H3K36me2	9B-H3K36me2.macs/9B-H3K36me2.bedGraph	9B-H3K36me2.macs/9B-H3K36me2.npeaks.bedGraph	9B-H3K36me2.macs/9B-H3K36me2.summits.bedGraph
9B-NSD2	9B-NSD2.macs/9B-NSD2.bedGraph	9B-NSD2.macs/9B-NSD2.npeaks.bedGraph	9B-NSD2.macs/9B-NSD2.summits.bedGraph

Table 8. Results of peak detection with MACS.

The following tables shows the number of peaks found for each condition, and their classification.

Condition	Total	Upstream	Exon	CodingExon	Intron	Downstream	Intergenic
2C-EZH2	23589	20.09%	7.25%	2.95%	26.95%	7.47%	35.30%
2C-H2AK119ub	22497	9.36%	3.51%	0.81%	31.07%	7.57%	47.68%
2C-H3K27ac	66099	17.29%	7.48%	1.78%	43.44%	7.79%	22.23%
2C-H3K27me3	51226	20.28%	7.16%	2.54%	36.91%	8.61%	24.50%
2C-H3K36me2	10495	4.73%	1.53%	0.26%	25.68%	5.53%	62.28%
2C-NSD2	7352	4.58%	1.31%	0.19%	9.47%	4.56%	79.90%
9B-EZH2	29918	21.54%	8.18%	3.53%	33.04%	9.40%	24.31%
9B-H2AK119ub	24036	11.38%	4.07%	1.29%	30.38%	8.65%	44.23%
9B-H3K27ac	60425	19.21%	8.63%	2.28%	42.45%	8.33%	19.10%
9B-H3K27me3	66115	19.63%	7.13%	2.76%	38.36%	9.09%	23.03%
9B-H3K36me2	8388	5.65%	2.10%	0.41%	18.97%	6.59%	66.29%
9B-NSD2	5211	6.01%	1.65%	0.23%	9.92%	6.56%	75.63%

Table 9. Classification of peaks in genome regions

6. Peak finding
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).

Condition	Count	bedGraph	Classified
*Peaks*
2C-EZH2	18	2C-EZH2.tags.d/peaks.bedGraph	2C-EZH2-peaks-distr.xlsx
2C-H2AK119ub	938	2C-H2AK119ub.tags.d/peaks.bedGraph	2C-H2AK119ub-peaks-distr.xlsx
2C-H3K27ac	1,498	2C-H3K27ac.tags.d/peaks.bedGraph	2C-H3K27ac-peaks-distr.xlsx
2C-H3K27me3	122	2C-H3K27me3.tags.d/peaks.bedGraph	2C-H3K27me3-peaks-distr.xlsx
2C-H3K36me2	1,894	2C-H3K36me2.tags.d/peaks.bedGraph	2C-H3K36me2-peaks-distr.xlsx
2C-NSD2	1	2C-NSD2.tags.d/peaks.bedGraph	2C-NSD2-peaks-distr.xlsx
9B-EZH2	788	9B-EZH2.tags.d/peaks.bedGraph	9B-EZH2-peaks-distr.xlsx
9B-H2AK119ub	0	9B-H2AK119ub.tags.d/peaks.bedGraph	9B-H2AK119ub-peaks-distr.xlsx
9B-H3K27ac	2,343	9B-H3K27ac.tags.d/peaks.bedGraph	9B-H3K27ac-peaks-distr.xlsx
9B-H3K27me3	1,377	9B-H3K27me3.tags.d/peaks.bedGraph	9B-H3K27me3-peaks-distr.xlsx
9B-H3K36me2	783	9B-H3K36me2.tags.d/peaks.bedGraph	9B-H3K36me2-peaks-distr.xlsx
9B-NSD2	278	9B-NSD2.tags.d/peaks.bedGraph	9B-NSD2-peaks-distr.xlsx
Combined	10,040	peaks.xlsx
*Regions*
2C-EZH2	26	2C-EZH2.tags.d/regions.bedGraph	2C-EZH2-regions-distr.xlsx
2C-H2AK119ub	57	2C-H2AK119ub.tags.d/regions.bedGraph	2C-H2AK119ub-regions-distr.xlsx
2C-H3K27ac	563	2C-H3K27ac.tags.d/regions.bedGraph	2C-H3K27ac-regions-distr.xlsx
2C-H3K27me3	57	2C-H3K27me3.tags.d/regions.bedGraph	2C-H3K27me3-regions-distr.xlsx
2C-H3K36me2	1,207	2C-H3K36me2.tags.d/regions.bedGraph	2C-H3K36me2-regions-distr.xlsx
2C-NSD2	1	2C-NSD2.tags.d/regions.bedGraph	2C-NSD2-regions-distr.xlsx
9B-EZH2	356	9B-EZH2.tags.d/regions.bedGraph	9B-EZH2-regions-distr.xlsx
9B-H2AK119ub	96	9B-H2AK119ub.tags.d/regions.bedGraph	9B-H2AK119ub-regions-distr.xlsx
9B-H3K27ac	180	9B-H3K27ac.tags.d/regions.bedGraph	9B-H3K27ac-regions-distr.xlsx
9B-H3K27me3	46	9B-H3K27me3.tags.d/regions.bedGraph	9B-H3K27me3-regions-distr.xlsx
9B-H3K36me2	733	9B-H3K36me2.tags.d/regions.bedGraph	9B-H3K36me2-regions-distr.xlsx
9B-NSD2	303	9B-NSD2.tags.d/regions.bedGraph	9B-NSD2-regions-distr.xlsx
Combined	3,625	regions.xlsx
*Enhancers*
2C-EZH2	6	2C-EZH2.tags.d/superEnhancers.bedGraph	2C-EZH2-enhancers-distr.xlsx
2C-H2AK119ub	82	2C-H2AK119ub.tags.d/superEnhancers.bedGraph	2C-H2AK119ub-enhancers-distr.xlsx
2C-H3K27ac	94	2C-H3K27ac.tags.d/superEnhancers.bedGraph	2C-H3K27ac-enhancers-distr.xlsx
2C-H3K27me3	10	2C-H3K27me3.tags.d/superEnhancers.bedGraph	2C-H3K27me3-enhancers-distr.xlsx
2C-H3K36me2	76	2C-H3K36me2.tags.d/superEnhancers.bedGraph	2C-H3K36me2-enhancers-distr.xlsx
2C-NSD2	1	2C-NSD2.tags.d/superEnhancers.bedGraph	2C-NSD2-enhancers-distr.xlsx
9B-EZH2	39	9B-EZH2.tags.d/superEnhancers.bedGraph	9B-EZH2-enhancers-distr.xlsx
9B-H2AK119ub	0	9B-H2AK119ub.tags.d/superEnhancers.bedGraph	9B-H2AK119ub-enhancers-distr.xlsx
9B-H3K27ac	188	9B-H3K27ac.tags.d/superEnhancers.bedGraph	9B-H3K27ac-enhancers-distr.xlsx
9B-H3K27me3	67	9B-H3K27me3.tags.d/superEnhancers.bedGraph	9B-H3K27me3-enhancers-distr.xlsx
9B-H3K36me2	40	9B-H3K36me2.tags.d/superEnhancers.bedGraph	9B-H3K36me2-enhancers-distr.xlsx
9B-NSD2	13	9B-NSD2.tags.d/superEnhancers.bedGraph	9B-NSD2-enhancers-distr.xlsx
Combined	616	enhancers.xlsx

Table 10. Results of peak detection with HOMER.

The following plots show the distribution of peak locations in the different conditions.

(png format, 37.91 kB)
Distribution of peak locations

(png format, 37.66 kB)
Distribution of region locations

(png format, 37.95 kB)
Distribution of enhancer locations

7. 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.

Test	Control	Test peaks	Control peaks	DiffPeaks
2C-EZH2	9B-EZH2	0	788	2C-EZH2.vs.9B-EZH2.diffPeaks.xlsx
2C-H2AK119ub	9B-H2AK119ub	0	0	2C-H2AK119ub.vs.9B-H2AK119ub.diffPeaks.xlsx
2C-H3K27ac	9B-H3K27ac	385	1020	2C-H3K27ac.vs.9B-H3K27ac.diffPeaks.xlsx
2C-H3K27me3	9B-H3K27me3	23	1194	2C-H3K27me3.vs.9B-H3K27me3.diffPeaks.xlsx
2C-H3K36me2	9B-H3K36me2	487	284	2C-H3K36me2.vs.9B-H3K36me2.diffPeaks.xlsx
2C-NSD2	9B-NSD2	0	278	2C-NSD2.vs.9B-NSD2.diffPeaks.xlsx

Table 11. Results of differential peak detection with HOMER.

8. 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.

Condition	Known	*de novo*
2C-EZH2	2C-EZH2.motifs/knownResults.html	2C-EZH2.motifs/homerResults.html
2C-H2AK119ub	2C-H2AK119ub.motifs/knownResults.html	2C-H2AK119ub.motifs/homerResults.html
2C-H3K27ac	2C-H3K27ac.motifs/knownResults.html	2C-H3K27ac.motifs/homerResults.html
2C-H3K27me3	2C-H3K27me3.motifs/knownResults.html	2C-H3K27me3.motifs/homerResults.html
2C-H3K36me2	2C-H3K36me2.motifs/knownResults.html	2C-H3K36me2.motifs/homerResults.html
2C-NSD2	2C-NSD2.motifs/knownResults.html	2C-NSD2.motifs/homerResults.html
9B-EZH2	9B-EZH2.motifs/knownResults.html	9B-EZH2.motifs/homerResults.html
9B-H2AK119ub	9B-H2AK119ub.motifs/knownResults.html	9B-H2AK119ub.motifs/homerResults.html
9B-H3K27ac	9B-H3K27ac.motifs/knownResults.html	9B-H3K27ac.motifs/homerResults.html
9B-H3K27me3	9B-H3K27me3.motifs/knownResults.html	9B-H3K27me3.motifs/homerResults.html
9B-H3K36me2	9B-H3K36me2.motifs/knownResults.html	9B-H3K36me2.motifs/homerResults.html
9B-NSD2	9B-NSD2.motifs/knownResults.html	9B-NSD2.motifs/homerResults.html

Table 12. Results of motif finding with HOMER.

9. Insert size distribution
Insert size distribution was analyzed using the Picard CollectInsertSizeMetrics tool. The following PDF files contain the plot of insert size distribution in each condition.

File: 2C-EZH2.insert-size-metrics.pdf
Size: 8.52 kB
Description: Insert size distribution in 2C-EZH2

File: 2C-H2AK119ub.insert-size-metrics.pdf
Size: 8.14 kB
Description: Insert size distribution in 2C-H2AK119ub

File: 2C-H3K27ac.insert-size-metrics.pdf
Size: 7.64 kB
Description: Insert size distribution in 2C-H3K27ac

File: 2C-H3K27me3.insert-size-metrics.pdf
Size: 8.19 kB
Description: Insert size distribution in 2C-H3K27me3

File: 2C-H3K36me2.insert-size-metrics.pdf
Size: 8.31 kB
Description: Insert size distribution in 2C-H3K36me2

File: 2C-NSD2.insert-size-metrics.pdf
Size: 8.15 kB
Description: Insert size distribution in 2C-NSD2

File: 9B-EZH2.insert-size-metrics.pdf
Size: 8.65 kB
Description: Insert size distribution in 9B-EZH2

File: 9B-H2AK119ub.insert-size-metrics.pdf
Size: 10.21 kB
Description: Insert size distribution in 9B-H2AK119ub

File: 9B-H3K27ac.insert-size-metrics.pdf
Size: 6.82 kB
Description: Insert size distribution in 9B-H3K27ac

File: 9B-H3K27me3.insert-size-metrics.pdf
Size: 6.88 kB
Description: Insert size distribution in 9B-H3K27me3

File: 9B-H3K36me2.insert-size-metrics.pdf
Size: 8.60 kB
Description: Insert size distribution in 9B-H3K36me2

File: 9B-NSD2.insert-size-metrics.pdf
Size: 7.02 kB
Description: Insert size distribution in 9B-NSD2

10. MultiQC report
MultiQC is a general Quality Control tool for a large number of bioinformatics pipeline. The report on this analysis (generated using MultiQC version 1.1) is available here:

MultiQC report

11. 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/NSD2//NSD2_CS_RCHACV_070218_Mohammad/hub/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/NSD2//NSD2_CS_RCHACV_070218_Mohammad/hub/hub.json.

Completed: 8-29-2018@11:01