QC Report

	general
Report generated at	2021-03-29 10:31:34
Title	max_mcf7
Description	chipseq of max_mcf7
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	12228305	46516156	31096045	33759185	30316568	7983930
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	11941764	44816011	28706371	32478002	28153114	4138229
Mapped Reads (QC-failed)	0	0	0	0	0	0
% Mapped Reads	97.7	96.3	92.30000000000001	96.2	92.9	51.800000000000004
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	10377792	38486400	22879927	26195707	22560055	3319095
Paired Reads	0	0	0	0	0	0
Unmapped Reads	0	0	0	0	0	0
Unpaired Duplicate Reads	358544	2048755	846441	582129	813034	20765
Paired Duplicate Reads	0	0	0	0	0	0
Paired Optical Duplicate Reads	0	0	0	0	0	0
% Duplicate Reads	3.4549000000000003	5.323300000000001	3.6995	2.2222	3.6039000000000003	0.6256

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	10377792	38486400	22879927	26195707	22560055	3319095
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	10377792	38486400	22879927	26195707	22560055	3319095
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	10363085	38393870	22255950	25876528	21948765	3296444
Distinct Fragments	10009352	36416264	22009026	25589391	21722498	3284913
Positions with Two Read	324920	1413183	221084	262485	203323	11230
NRF = Distinct/Total	0.965866	0.948492	0.988905	0.988904	0.989691	0.996502
PBC1 = OneRead/Distinct	0.966219	0.955346	0.989564	0.98933	0.9903	0.99654
PBC2 = OneRead/TwoRead	29.764948	24.618275	98.511643	96.448776	105.801011	291.500089

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	41293	13605
N1	27260	7762
N2	67910	27963
Np	63048	27679
N optimal	63048	27679
N conservative	41293	13605
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.5268447436611532	2.0344726203601615
Self Consistency Ratio	2.491195891415994	3.6025508889461477
Reproducibility Test	borderline	fail

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	84758	143752

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	120.0	90.0	105.0	105.0
25 percentile	120.0	107.0	296.0	206.0
50 percentile (median)	150.0	152.0	449.0	298.0
75 percentile	247.0	252.0	697.0	475.0
Max size	2950.0	3389.0	3546.0	3546.0
Mean	219.21806791099365	224.63073905058712	543.4482459626431	392.69875333079557

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	10363169	15000000
Estimated Fragment Length	120	90
Cross-correlation at Estimated Fragment Length	0.159287146838019	0.252373011715854
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.1547952	0.2426713
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.1284374	0.1765771
NSC (Normalized Strand Cross-correlation coeff.)	1.240193	1.429251
RSC (Relative Strand Cross-correlation coeff.)	1.17042	1.146786

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	0.1808940563403255	0.19609334022703787
Synthetic AUC	0.4845562623580995	0.49198881680055656
X-intercept	0.339354619429394	0.14926325049483175
Synthetic X-intercept	4.3971288080457287e-35	5.740772811917672e-133
Elbow Point	0.6370394066017554	0.7159665713657356
Synthetic Elbow Point	0.5052409538236415	0.5097359794179958
JS Distance	0.16102306294502516	0.18768049849467036
Synthetic JS Distance	0.32638716846397287	0.41043556317105534
% Genome Enriched	35.935182038107044	25.43835096067337
Diff. Enrichment	25.98576526082466	19.582278656191974
CHANCE Divergence	0.2426154918819619	0.1694980035716796

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	0.13304226949239298	0.2041442431612206	0.1651574824394245	0.19729145880103102	0.16520065154514563	0.1975168371164879	0.1945547365236286	0.18070197497586782	0.18088546312195236

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	0.1437766329994774	0.09375828692654468	0.1726686309969236	0.16752848384354743

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	0.09592511015018933	0.05486041732191202	0.13146989585931654	0.12991370040458255

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