QC Report

	general
Report generated at	2021-03-30 08:19:42
Title	gabpa_mcf7
Description	chipseq of gabpa_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	33360202	31789673	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	30560469	20254153	28706371	32478002	28153114	4138229
Mapped Reads (QC-failed)	0	0	0	0	0	0
% Mapped Reads	91.60000000000001	63.7	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	26019754	17399342	22879927	26195707	22560055	3319095
Paired Reads	0	0	0	0	0	0
Unmapped Reads	0	0	0	0	0	0
Unpaired Duplicate Reads	3014998	4937006	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	11.5873	28.374700000000004	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	26019754	17399342	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	26019754	17399342	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	25890160	17348593	22255950	25876528	21948765	3296444
Distinct Fragments	22982568	12450402	22009026	25589391	21722498	3284913
Positions with Two Read	1160135	2472471	221084	262485	203323	11230
NRF = Distinct/Total	0.887695	0.717661	0.988905	0.988904	0.989691	0.996502
PBC1 = OneRead/Distinct	0.932972	0.729725	0.989564	0.98933	0.9903	0.99654
PBC2 = OneRead/TwoRead	18.48242	3.674609	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	14858	6582
N1	19777	7258
N2	17360	6336
Np	19465	4281
N optimal	19465	6582
N conservative	14858	6582
Optimal Set	pooled-pr1_vs_pooled-pr2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.3100686498855836	1.5374912403644008
Self Consistency Ratio	1.1392281105990782	1.1455176767676767
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	70736	151149

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	185.0	150.0	150.0
25 percentile	115.0	185.0	457.25	258.0
50 percentile (median)	148.0	185.0	692.0	358.0
75 percentile	219.0	210.0	1001.0	575.0
Max size	4158.0	4384.0	4362.0	4362.0
Mean	205.39804342908843	231.55684126259519	763.7365542388332	476.1806832776779

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	185
Cross-correlation at Estimated Fragment Length	0.286321463362581	0.22883664669016
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.2455024	0.178397
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.1453057	0.1053616
NSC (Normalized Strand Cross-correlation coeff.)	1.970477	2.171916
RSC (Relative Strand Cross-correlation coeff.)	1.407389	1.690619

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	0.18828806397756143	0.1702234163156808
Synthetic AUC	0.4903964719466002	0.4882581014381453
X-intercept	0.1861362027806768	0.2854532295277968
Synthetic X-intercept	3.741150580270082e-92	2.689942897522822e-61
Elbow Point	0.7147786934737667	0.6591511618142777
Synthetic Elbow Point	0.49372363469468944	0.5072623851259332
JS Distance	0.21056593909378438	0.2036560420425857
Synthetic JS Distance	0.4210289294242251	0.4072213092268085
% Genome Enriched	25.38157331765854	30.68161370425019
Diff. Enrichment	21.322190217000585	27.642545538021974
CHANCE Divergence	0.18456443332990452	0.24680379854932194

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	0.17339149324778397	0.2108321107775225	0.171661423086475	0.21143167368053345	0.17194097991856494	0.21163788837531902	0.17271009050948458	0.1717459985809009	0.1717320876510188

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	0.151127190672049	0.1516596967058182	0.15534420784418168	0.15645215183660202

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	0.1386009971280839	0.13392098172795946	0.14413625526758425	0.13102036947061266

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