QC Report

	general
Report generated at	2021-06-17 23:39:42
Title	max_k562_3
Description	chipseq of max_k562_3
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}, 'ctl4': {'paired_end': False}}
Peak caller	macs2

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2	ctl3	ctl4
Total Reads	40637825	27439953	14592598	37802089	46386603	58513882
Total Reads (QC-failed)	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0
Mapped Reads	36278157	22644005	11534792	26787747	30160217	53350276
Mapped Reads (QC-failed)	0	0	0	0	0	0
% Mapped Reads	89.3	82.5	79.0	70.89999999999999	65.0	91.2
Paired Reads	0	0	0	0	0	0
Paired Reads (QC-failed)	0	0	0	0	0	0
Read1	0	0	0	0	0	0
Read1 (QC-failed)	0	0	0	0	0	0
Read2	0	0	0	0	0	0
Read2 (QC-failed)	0	0	0	0	0	0
Properly Paired Reads	0	0	0	0	0	0
Properly Paired Reads (QC-failed)	0	0	0	0	0	0
% Properly Paired Reads	0.0	0.0	0.0	0.0	0.0	0.0
With itself	0	0	0	0	0	0
With itself (QC-failed)	0	0	0	0	0	0
Singletons	0	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0	0
Diff. Chroms (QC-failed)	0	0	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2	ctl3	ctl4
Unpaired Reads	29227086	17828957	9070521	20456589	22577943	37531213
Paired Reads	0	0	0	0	0	0
Unmapped Reads	0	0	0	0	0	0
Unpaired Duplicate Reads	3009469	5662904	395125	1638697	907434	2089922
Paired Duplicate Reads	0	0	0	0	0	0
Paired Optical Duplicate Reads	0	0	0	0	0	0
% Duplicate Reads	10.296800000000001	31.762400000000003	4.3561000000000005	8.0106	4.0191	5.5685

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	ctl4
Total Reads	29227086	17828957	9070521	20456589	22577943	37531213
Total Reads (QC-failed)	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0
Mapped Reads	29227086	17828957	9070521	20456589	22577943	37531213
Mapped Reads (QC-failed)	0	0	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0	100.0	100.0
Paired Reads	0	0	0	0	0	0
Paired Reads (QC-failed)	0	0	0	0	0	0
Read1	0	0	0	0	0	0
Read1 (QC-failed)	0	0	0	0	0	0
Read2	0	0	0	0	0	0
Read2 (QC-failed)	0	0	0	0	0	0
Properly Paired Reads	0	0	0	0	0	0
Properly Paired Reads (QC-failed)	0	0	0	0	0	0
% Properly Paired Reads	0.0	0.0	0.0	0.0	0.0	0.0
With itself	0	0	0	0	0	0
With itself (QC-failed)	0	0	0	0	0	0
Singletons	0	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0	0
Diff. Chroms (QC-failed)	0	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	ctl4
Total Fragments	29193502	17806503	8981533	20288786	22366071	37282196
Distinct Fragments	26203057	12157118	8658772	18799594	21650523	35423636
Positions with Two Read	1712144	2806375	295814	1282093	651107	1599314
NRF = Distinct/Total	0.897565	0.682735	0.964064	0.9266	0.968007	0.950149
PBC1 = OneRead/Distinct	0.91673	0.673325	0.964589	0.927184	0.968898	0.951651
PBC2 = OneRead/TwoRead	14.029846	2.916819	28.234485	13.595486	32.217679	21.078369

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	110578	39289
N1	98020	41818
N2	153161	49184
Np	120054	52034
N optimal	120054	52034
N conservative	110578	39289
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0856951654036064	1.3243910509302859
Self Consistency Ratio	1.5625484594980616	1.176144244105409
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	196567	499658

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	115.0	100.0	108.0	108.0
25 percentile	132.0	100.0	243.0	178.0
50 percentile (median)	176.0	100.0	355.0	238.0
75 percentile	262.0	141.0	588.0	368.0
Max size	4081.0	3024.0	4262.0	4262.0
Mean	250.75662242390635	143.7977416552922	482.6347003882077	334.9356289669649

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	15000000	15000000
Estimated Fragment Length	115	100
Cross-correlation at Estimated Fragment Length	0.388867711473095	0.272589722925284
Phantom Peak	40	40
Cross-correlation at Phantom Peak	0.3136792	0.2230122
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.1470524	0.1091722
NSC (Normalized Strand Cross-correlation coeff.)	2.644416	2.496879
RSC (Relative Strand Cross-correlation coeff.)	1.451239	1.435502

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	0.12245155673840895	0.11166865620046529
Synthetic AUC	0.4892235184348936	0.4861934097308596
X-intercept	0.28832712208697875	0.426652644711377
Synthetic X-intercept	5.796446980078249e-73	4.336443553981692e-44
Elbow Point	0.7804937540986229	0.7281733337598567
Synthetic Elbow Point	0.505636455866436	0.5062985212733386
JS Distance	0.3661515925964915	0.3142868427241992
Synthetic JS Distance	0.5108759368946273	0.4627961059687939
% Genome Enriched	13.293333439964172	19.683986180643302
Diff. Enrichment	45.50642756206823	47.14790267085554
CHANCE Divergence	0.39590049288332285	0.41019575113593854

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	0.4253922200796891	0.4665520254493855	0.40693252827189136	0.4715933483044831	0.4068046332090719	0.4716064137462676	0.4255009287542516	0.403895066062077	0.40390082106778125

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	0.3722462596355584	0.38131451079317313	0.345455934410521	0.38091889706918197

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	0.30065462580438396	0.31992084328899567	0.2744339447338395	0.32313535160616885

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