QC Report

	general
Report generated at	2021-06-18 03:32:38
Title	e2f1_k562
Description	chipseq of e2f1_k562
Pipeline version	v1.3.6
Pipeline type	tf
Genome	hg38
Aligner	bowtie2
Sequencing endedness	{'rep1': {'paired_end': True}, 'rep2': {'paired_end': True}, 'ctl1': {'paired_end': True}, 'ctl2': {'paired_end': True}}
Peak caller	macs2

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2
Total Reads	36970146	54097182	90517746	95213346
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	36092756	53191986	89458661	94154887
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	97.6	98.3	98.8	98.9
Paired Reads	36970146	54097182	90517746	95213346
Paired Reads (QC-failed)	0	0	0	0
Read1	18485073	27048591	45258873	47606673
Read1 (QC-failed)	0	0	0	0
Read2	18485073	27048591	45258873	47606673
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	35494628	52639924	88889944	93535642
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	96.0	97.3	98.2	98.2
With itself	35813462	52821266	89037122	93722754
With itself (QC-failed)	0	0	0	0
Singletons	279294	370720	421539	432133
Singletons (QC-failed)	0	0	0	0
% Singleton	0.8	0.7000000000000001	0.5	0.5
Diff. Chroms	214948	76430	38020	40990
Diff. Chroms (QC-failed)	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2
Unpaired Reads	0	0	0	0
Paired Reads	15362095	22806655	37410880	39565402
Unmapped Reads	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0
Paired Duplicate Reads	2313548	2591978	2744207	2210699
Paired Optical Duplicate Reads	0	0	0	0
% Duplicate Reads	15.060100000000002	11.365	7.3353	5.5875

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8, for paired-end)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

SAMstat (filtered/deduped BAM)

	rep1	rep2	ctl1	ctl2
Total Reads	26097094	40429354	69333346	74709406
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	26097094	40429354	69333346	74709406
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0
Paired Reads	26097094	40429354	69333346	74709406
Paired Reads (QC-failed)	0	0	0	0
Read1	13048547	20214677	34666673	37354703
Read1 (QC-failed)	0	0	0	0
Read2	13048547	20214677	34666673	37354703
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	26097094	40429354	69333346	74709406
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	100.0	100.0	100.0	100.0
With itself	26097094	40429354	69333346	74709406
With itself (QC-failed)	0	0	0	0
Singletons	0	0	0	0
Singletons (QC-failed)	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0
Diff. Chroms (QC-failed)	0	0	0	0

Filtered and duplicates removed

Sequence quality metrics (filtered/deduped BAM)

Open chromatin assays are known to have significant GC bias. Please take this into consideration as necessary.

Library complexity quality metrics

Library complexity (filtered non-mito BAM)

	rep1	rep2	ctl1	ctl2
Total Fragments	15293622	22708695	36686094	38983260
Distinct Fragments	12992703	20132721	34174655	36939155
Positions with Two Read	1687416	2099248	2235543	1866995
NRF = Distinct/Total	0.84955	0.886564	0.931542	0.947565
PBC1 = OneRead/Distinct	0.848277	0.884434	0.930658	0.947118
PBC2 = OneRead/TwoRead	6.531533	8.482111	14.226924	18.739069

Mitochondrial reads are filtered out by default. The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads in a dataset; it is the ratio between the number of positions in the genome that uniquely mapped reads map to and the total number of uniquely mappable reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with AT LEAST one read pair. PBC1 is the primary measure, and the PBC1 should be close to 1. Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking, 0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with EXACTLY two read pairs. The PBC2 should be significantly greater than 1. See more details at the ENCODE portal standard for ChIP-Seq pipeline

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally

0-0.5 is severe bottlenecking
0.5-0.8 is moderate bottlenecking
0.8-0.9 is mild bottlenecking
0.9-1.0 is no bottlenecking

Replication quality metrics

IDR (Irreproducible Discovery Rate) plots

Reproducibility QC and peak detection statistics

	overlap	idr
Nt	11167	3966
N1	8248	2729
N2	11598	3062
Np	13011	4303
N optimal	13011	4303
N conservative	11167	3966
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.1651293991224143	1.0849722642460917
Self Consistency Ratio	1.4061590688651795	1.1220227189446683
Reproducibility Test	pass	pass

Reproducibility QC

N1: Replicate 1 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Ni: Replicate i self-consistent peaks (comparing two pseudoreplicates generated by subsampling RepX reads)
Nt: True Replicate consistent peaks (comparing true replicates Rep1 vs Rep2)
Np: Pooled-pseudoreplicate consistent peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2)
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'

Number of raw peaks

	rep1	rep2
Number of peaks	83067	86737

Top 500000 raw peaks from macs2 with p-val threshold 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	280.0	260.0	270.0	270.0
25 percentile	290.0	276.0	508.5	439.0
50 percentile (median)	338.0	327.0	672.0	559.0
75 percentile	425.0	423.0	958.5	773.5
Max size	2663.0	12441.0	7401.0	7401.0
Mean	384.50100521265966	391.72484637467284	802.4443411573321	674.2460225962647

Enrichment / Signal-to-noise ratio

Strand cross-correlation measures (trimmed/filtered SE BAM)

	rep1	rep2
Number of Subsampled Reads	15000000	15000000
Estimated Fragment Length	280	260
Cross-correlation at Estimated Fragment Length	0.147486580710653	0.164431317021041
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.1417677	0.1595346
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.1350188	0.1522453
NSC (Normalized Strand Cross-correlation coeff.)	1.092341	1.080042
RSC (Relative Strand Cross-correlation coeff.)	1.847382	1.67177

Performed on subsampled (15000000) reads mapped from FASTQs that are trimmed to 50. Such FASTQ trimming and subsampling reads are for cross-corrleation analysis only. Untrimmed FASTQs are used for all the other analyses.

NOTE1: For SE datasets, reads from replicates are randomly subsampled to 15000000.
NOTE2: For PE datasets, the first end (R1) of each read-pair is selected and trimmed to 50 the reads are then randomly subsampled to 15000000.

Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value

Jensen-Shannon distance (filtered/deduped BAM)

	rep1	rep2
AUC	0.23633812460838696	0.2541264256445102
Synthetic AUC	0.49312836210513183	0.4944757577280508
X-intercept	0.19247817246501697	0.14458855071565524
Synthetic X-intercept	3.11463961112624e-181	2.7187894554296975e-281
Elbow Point	0.6094455696151916	0.6006945624596388
Synthetic Elbow Point	0.49977294378101406	0.5024694107328719
JS Distance	0.07320272323089679	0.06843399979678153
Synthetic JS Distance	0.3071257035648663	0.3039935539632196
% Genome Enriched	35.92011532056037	37.399609333607906
Diff. Enrichment	18.205276647119124	14.01087480679431
CHANCE Divergence	0.16226241114268117	0.12518287867252587

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for macs2 raw peaks

	rep1	rep2	rep1-pr1	rep2-pr1	rep1-pr2	rep2-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.07531957389585216	0.0737434736157298	0.08000376746899349	0.07731857019933733	0.08019276630515002	0.07711545809589034	0.06657698003055867	0.06825859283762796	0.06803910938032401

FRiP for overlap peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.02968303673750927	0.026441756312024625	0.029964911138575204	0.03196152904480937

FRiP for IDR peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.02049945609601763	0.01798418628526226	0.017918960565137896	0.021312561283897195

For macs2 raw peaks:

repX: Peak from true replicate X
repX-prY: Peak from Yth pseudoreplicates from replicate X
pooled: Peak from pooled true replicates (pool of rep1, rep2, ...)
pooled-pr1: Peak from 1st pooled pseudo replicate (pool of rep1-pr1, rep2-pr1, ...)
pooled-pr2: Peak from 2nd pooled pseudo replicate (pool of rep1-pr2, rep2-pr2, ...)

For overlap/IDR peaks:

repX_vs_repY: Comparing two peaks from true replicates X and Y
repX-pr1_vs_repX-pr2: Comparing two peaks from both pseudoreplicates from replicate X
pooled-pr1_vs_pooled-pr2: Comparing two peaks from 1st and 2nd pooled pseudo replicates