QC Report

	general
Report generated at	2021-06-18 06:42:45
Title	elk1_mcf7
Description	chipseq of elk1_mcf7
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}, 'ctl3': {'paired_end': True}, 'ctl4': {'paired_end': True}}
Peak caller	macs2

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2	ctl3	ctl4
Total Reads	54126898	59885482	84627162	76248808	95057392	74249076
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	53249913	58139921	83659980	75224580	93953972	73318003
Mapped Reads (QC-failed)	0	0	0	0	0	0
% Mapped Reads	98.4	97.1	98.9	98.7	98.8	98.7
Paired Reads	54126898	59885482	84627162	76248808	95057392	74249076
Paired Reads (QC-failed)	0	0	0	0	0	0
Read1	27063449	29942741	42313581	38124404	47528696	37124538
Read1 (QC-failed)	0	0	0	0	0	0
Read2	27063449	29942741	42313581	38124404	47528696	37124538
Read2 (QC-failed)	0	0	0	0	0	0
Properly Paired Reads	52940492	57449348	82963266	74709426	93370194	72662486
Properly Paired Reads (QC-failed)	0	0	0	0	0	0
% Properly Paired Reads	97.8	95.89999999999999	98.0	98.0	98.2	97.89999999999999
With itself	53003776	57643280	83218732	74899394	93543018	72927882
With itself (QC-failed)	0	0	0	0	0	0
Singletons	246137	496641	441248	325186	410954	390121
Singletons (QC-failed)	0	0	0	0	0	0
% Singleton	0.5	0.8	0.5	0.4	0.4	0.5
Diff. Chroms	16345	50989	94670	40215	46923	105767
Diff. Chroms (QC-failed)	0	0	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2	ctl3	ctl4
Unpaired Reads	0	0	0	0	0	0
Paired Reads	22823043	24797589	35879435	32098563	40056778	31368006
Unmapped Reads	0	0	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0	0	0
Paired Duplicate Reads	1480471	1660288	2654761	1452621	4134970	1629469
Paired Optical Duplicate Reads	0	0	0	0	0	0
% Duplicate Reads	6.486699999999999	6.6954	7.3991	4.5255	10.3228	5.1947

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	42685144	46274602	66449348	61291884	71843616	59477074
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	42685144	46274602	66449348	61291884	71843616	59477074
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	42685144	46274602	66449348	61291884	71843616	59477074
Paired Reads (QC-failed)	0	0	0	0	0	0
Read1	21342572	23137301	33224674	30645942	35921808	29738537
Read1 (QC-failed)	0	0	0	0	0	0
Read2	21342572	23137301	33224674	30645942	35921808	29738537
Read2 (QC-failed)	0	0	0	0	0	0
Properly Paired Reads	42685144	46274602	66449348	61291884	71843616	59477074
Properly Paired Reads (QC-failed)	0	0	0	0	0	0
% Properly Paired Reads	100.0	100.0	100.0	100.0	100.0	100.0
With itself	42685144	46274602	66449348	61291884	71843616	59477074
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	22802808	24756209	35728511	32041408	39973217	31260020
Distinct Fragments	21323959	23099681	33094746	30593422	35849689	29641184
Positions with Two Read	1324464	1478564	2330231	1337442	3431752	1482945
NRF = Distinct/Total	0.935146	0.933086	0.926284	0.954809	0.896843	0.948214
PBC1 = OneRead/Distinct	0.934354	0.932234	0.925124	0.954509	0.895025	0.947723
PBC2 = OneRead/TwoRead	15.043166	14.564344	13.138933	21.833994	9.349845	18.943137

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	11726	3116
N1	9477	1675
N2	19770	4771
Np	15617	4567
N optimal	15617	4567
N conservative	11726	3116
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.3318267098754903	1.465661103979461
Self Consistency Ratio	2.0861031972143085	2.848358208955224
Reproducibility Test	borderline	borderline

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	117777	127732

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	205.0	235.0	220.0	220.0
25 percentile	214.0	253.0	515.0	387.0
50 percentile (median)	253.0	309.0	678.0	510.0
75 percentile	317.0	412.0	909.0	707.0
Max size	1770.0	4241.0	4541.0	4541.0
Mean	281.6621836181937	372.4228854163405	746.9244580687541	584.7950310559006

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	15000000	15000000
Estimated Fragment Length	205	235
Cross-correlation at Estimated Fragment Length	0.171449869406974	0.179434619737545
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.1700305	0.1753092
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.1662562	0.1689145
NSC (Normalized Strand Cross-correlation coeff.)	1.031239	1.062281
RSC (Relative Strand Cross-correlation coeff.)	1.376061	1.645136

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	0.27218606729455136	0.2637342350198229
Synthetic AUC	0.4946302144337059	0.4948475932403476
X-intercept	0.13324563052057883	0.12821138243891125
Synthetic X-intercept	8.78873769694554e-298	0.0
Elbow Point	0.5740862179961373	0.5966403691515353
Synthetic Elbow Point	0.501987182502938	0.5083840863707134
JS Distance	0.03171717792732178	0.048990063300817684
Synthetic JS Distance	0.2814559072916413	0.3008991891654589
% Genome Enriched	37.65289679191641	34.64234446412648
Diff. Enrichment	14.599976487303639	15.908562479103171
CHANCE Divergence	0.1281224895351793	0.1378652225338505

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	0.05793746414443395	0.09372720266724283	0.07954851926937391	0.09744204402051718	0.07969864175695413	0.09756752084296785	0.06355824127465472	0.06326324125828234	0.06339543872788123

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	0.018971400840105818	0.00994116360483638	0.03924446503073111	0.025008816909166984

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	0.011301223814195693	0.004382976897067513	0.021277697861129093	0.014491914129341152

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