QC Report

	general
Report generated at	2021-03-27 22:54:58
Title	max_hepg2_2
Description	chipseq of max_hepg2_2
Pipeline version	v1.3.6
Pipeline type	tf
Genome	hg38
Aligner	bowtie2
Sequencing endedness	{'rep1': {'paired_end': False}, 'rep2': {'paired_end': False}, 'ctl1': {'paired_end': False}, 'ctl2': {'paired_end': False}, 'ctl3': {'paired_end': False}}
Peak caller	macs2

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2	ctl3
Total Reads	31679169	38097616	45541199	33941892	58536426
Total Reads (QC-failed)	0	0	0	0	0
Duplicate Reads	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0
Mapped Reads	30193378	35690598	44383897	32679514	46692008
Mapped Reads (QC-failed)	0	0	0	0	0
% Mapped Reads	95.3	93.7	97.5	96.3	79.80000000000001
Paired Reads	0	0	0	0	0
Paired Reads (QC-failed)	0	0	0	0	0
Read1	0	0	0	0	0
Read1 (QC-failed)	0	0	0	0	0
Read2	0	0	0	0	0
Read2 (QC-failed)	0	0	0	0	0
Properly Paired Reads	0	0	0	0	0
Properly Paired Reads (QC-failed)	0	0	0	0	0
% Properly Paired Reads	0.0	0.0	0.0	0.0	0.0
With itself	0	0	0	0	0
With itself (QC-failed)	0	0	0	0	0
Singletons	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0
Diff. Chroms (QC-failed)	0	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2	ctl3
Unpaired Reads	26054431	30754043	37159035	26937599	37055800
Paired Reads	0	0	0	0	0
Unmapped Reads	0	0	0	0	0
Unpaired Duplicate Reads	1390910	2027160	3078272	2169423	827433
Paired Duplicate Reads	0	0	0	0	0
Paired Optical Duplicate Reads	0	0	0	0	0
% Duplicate Reads	5.3385	6.5915	8.283999999999999	8.0535	2.2329000000000003

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	ctl3
Total Reads	26054431	30754043	37159035	26937599	37055800
Total Reads (QC-failed)	0	0	0	0	0
Duplicate Reads	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0
Mapped Reads	26054431	30754043	37159035	26937599	37055800
Mapped Reads (QC-failed)	0	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0	100.0
Paired Reads	0	0	0	0	0
Paired Reads (QC-failed)	0	0	0	0	0
Read1	0	0	0	0	0
Read1 (QC-failed)	0	0	0	0	0
Read2	0	0	0	0	0
Read2 (QC-failed)	0	0	0	0	0
Properly Paired Reads	0	0	0	0	0
Properly Paired Reads (QC-failed)	0	0	0	0	0
% Properly Paired Reads	0.0	0.0	0.0	0.0	0.0
With itself	0	0	0	0	0
With itself (QC-failed)	0	0	0	0	0
Singletons	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0
Diff. Chroms (QC-failed)	0	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	ctl3
Total Fragments	25734952	30282513	34448504	25164627	36811513
Distinct Fragments	24640507	28703813	34056783	24744074	36207296
Positions with Two Read	788366	1260765	352839	374800	533242
NRF = Distinct/Total	0.957472	0.947868	0.988629	0.983288	0.983586
PBC1 = OneRead/Distinct	0.9629	0.951443	0.989366	0.984186	0.984805
PBC2 = OneRead/TwoRead	30.095589	21.661483	95.495762	64.97539	66.868551

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	51400	18655
N1	52843	22371
N2	41010	16420
Np	59447	27596
N optimal	59447	27596
N conservative	51400	18655
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.156556420233463	1.4792816939158402
Self Consistency Ratio	1.2885393806388685	1.3624238733252132
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	126081	104968

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	95.0	110.0	102.0	102.0
25 percentile	110.0	117.0	294.0	204.0
50 percentile (median)	156.0	163.0	445.0	299.0
75 percentile	267.0	257.0	679.0	477.0
Max size	4005.0	2464.0	4019.0	4019.0
Mean	242.19672274172953	223.67653951680512	532.8427308305552	390.63306811109055

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	15000000	15000000
Estimated Fragment Length	95	110
Cross-correlation at Estimated Fragment Length	0.2929623409507	0.238157564223122
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.2792782	0.2254051
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.1731528	0.1687797
NSC (Normalized Strand Cross-correlation coeff.)	1.691929	1.411056
RSC (Relative Strand Cross-correlation coeff.)	1.128943	1.225207

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	0.1531941662985662	0.20597573422922907
Synthetic AUC	0.4903007969251005	0.49107253056064765
X-intercept	0.22980786532578923	0.14381110422456364
Synthetic X-intercept	2.5320928357453187e-90	8.007602666989459e-107
Elbow Point	0.7659295839414599	0.6919047523841894
Synthetic Elbow Point	0.5000942735418777	0.4961069849886901
JS Distance	0.23648010160120272	0.18140965674876455
Synthetic JS Distance	0.46276466458724386	0.3983698942558377
% Genome Enriched	21.47589819461383	41.80338684847152
Diff. Enrichment	16.892486879568995	9.581520409486444
CHANCE Divergence	0.14945421819988666	0.09624896396927521

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	0.2764274913545416	0.1742175492178378	0.25815024484126153	0.16266784296725334	0.2584459533369181	0.16288902772520114	0.2329542243996908	0.21565134047954393	0.21573159017549354

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	0.1936996934647461	0.23347924965239117	0.14088401320112612	0.20368559803243438

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	0.13565213879887003	0.1777047443484757	0.09808173839127428	0.16074506771648187

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