QC Report

	general
Report generated at	2021-06-08 01:58:37
Title	gabpa_mmcf7
Description	chipseq of gabpa_mmcf7
Pipeline version	v1.3.6
Pipeline type	tf
Genome	hg38
Aligner	bowtie2
Sequencing endedness	{'rep1': {'paired_end': False}, 'rep2': {'paired_end': False}, 'rep3': {'paired_end': False}, 'ctl1': {'paired_end': False}}
Peak caller	macs2

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	rep3	ctl1
Total Reads	21262617	27254246	23992812	23121759
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	19695764	25188587	22325670	22800983
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	92.60000000000001	92.4	93.10000000000001	98.6
Paired Reads	0	0	0	0
Paired Reads (QC-failed)	0	0	0	0
Read1	0	0	0	0
Read1 (QC-failed)	0	0	0	0
Read2	0	0	0	0
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	0	0	0	0
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	0.0	0.0	0.0	0.0
With itself	0	0	0	0
With itself (QC-failed)	0	0	0	0
Singletons	0	0	0	0
Singletons (QC-failed)	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0
Diff. Chroms (QC-failed)	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	rep3	ctl1
Unpaired Reads	16946305	21614354	19203446	19702321
Paired Reads	0	0	0	0
Unmapped Reads	0	0	0	0
Unpaired Duplicate Reads	298565	501842	354782	213368
Paired Duplicate Reads	0	0	0	0
Paired Optical Duplicate Reads	0	0	0	0
% Duplicate Reads	1.7618000000000003	2.3218	1.8475	1.083

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	rep3	ctl1
Total Reads	16946305	21614354	19203446	19702321
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	16946305	21614354	19203446	19702321
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0
Paired Reads	0	0	0	0
Paired Reads (QC-failed)	0	0	0	0
Read1	0	0	0	0
Read1 (QC-failed)	0	0	0	0
Read2	0	0	0	0
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	0	0	0	0
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	0.0	0.0	0.0	0.0
With itself	0	0	0	0
With itself (QC-failed)	0	0	0	0
Singletons	0	0	0	0
Singletons (QC-failed)	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0
Diff. Chroms (QC-failed)	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	rep3	ctl1
Total Fragments	16931750	21594744	19182090	19651464
Distinct Fragments	16637785	21100500	18835589	19468941
Positions with Two Read	275242	459969	323333	166997
NRF = Distinct/Total	0.982638	0.977113	0.981936	0.990712
PBC1 = OneRead/Distinct	0.983006	0.977552	0.98236	0.991162
PBC2 = OneRead/TwoRead	59.420579	44.843987	57.22684	115.552178

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	2573	1525
N1	2359	1667
N2	3012	1807
N3	2333	1650
Np	2491	1690
N optimal	2573	1690
N conservative	2573	1525
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0329185066238458	1.1081967213114754
Self Consistency Ratio	1.2910415773681954	1.0951515151515152
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	rep3
Number of peaks	27951	9338	13563

Top 500000 raw peaks from macs2 with p-val threshold 0.01

Peak calling statistics

Peak region size

	rep1	rep2	rep3	idr_opt	overlap_opt
Min size	195.0	175.0	230.0	214.0	200.0
25 percentile	195.0	175.0	230.0	389.0	319.0
50 percentile (median)	197.0	198.0	249.0	472.0	406.0
75 percentile	251.0	292.0	317.0	591.75	531.0
Max size	1884.0	1550.0	1858.0	2376.0	2376.0
Mean	244.64562985224143	266.7026129792247	301.2675661726757	502.2307692307692	438.198600855033

Enrichment / Signal-to-noise ratio

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

	rep1	rep2	rep3
Number of Subsampled Reads	15000000	15000000	15000000
Estimated Fragment Length	195	175	230
Cross-correlation at Estimated Fragment Length	0.17792439601785	0.177865837261828	0.177595562535884
Phantom Peak	50	50	50
Cross-correlation at Phantom Peak	0.1787318	0.1787395	0.178881
Argmin of Cross-correlation	1500	1500	1500
Minimum of Cross-correlation	0.1753804	0.1751678	0.1757774
NSC (Normalized Strand Cross-correlation coeff.)	1.014505	1.015402	1.010344
RSC (Relative Strand Cross-correlation coeff.)	0.7590732	0.7553859	0.5858216

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	rep3
AUC	0.2628178668885389	0.27444277169158177	0.270798985014296
Synthetic AUC	0.4877951450268079	0.4892021743732178	0.4885391813401501
X-intercept	0.17069332981450158	0.1404453721364507	0.1524353914500386
Synthetic X-intercept	1.1511926801978694e-56	1.149111327081419e-72	2.1656222653347666e-64
Elbow Point	0.5561753497838717	0.5748751414530376	0.6064686524074008
Synthetic Elbow Point	0.4986108104880323	0.49613285070113144	0.5014938831576645
JS Distance	0.03937007255691834	0.03116725257597453	0.018325068428497435
Synthetic JS Distance	0.25618306915122463	0.2574982792244423	0.2545967843858269
% Genome Enriched	41.12994485830704	40.48395932550393	35.74653215132576
Diff. Enrichment	18.348950028889156	15.505470478033633	16.70662939393394
CHANCE Divergence	0.16470094157675796	0.1380178218664857	0.1448878486659266

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for macs2 raw peaks

	rep1	rep2	rep3	rep1-pr1	rep2-pr1	rep3-pr1	rep1-pr2	rep2-pr2	rep3-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.016475981047195835	0.009028028318588656	0.010024815337830513	0.018249995013662566	0.023984061702699976	0.018391074185331112	0.018206565868286086	0.023960466271626717	0.018376285172984057	0.005829156359299603	0.006188722110578497	0.0061251880579676265

FRiP for overlap peaks

	rep1_vs_rep2	rep1_vs_rep3	rep2_vs_rep3	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	rep3-pr1_vs_rep3-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.005693154944580203	0.005578654771851827	0.005573824782708916	0.00589550347406116	0.006392742526563597	0.004770758331603609	0.005648455905271968

FRiP for IDR peaks

	rep1_vs_rep2	rep1_vs_rep3	rep2_vs_rep3	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	rep3-pr1_vs_rep3-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.004645895578231499	0.004488617974778628	0.004499195477883714	0.0051958819341443455	0.0054515161544962205	0.004262828661064269	0.004870429482115234

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