QC Report

	general
Report generated at	2021-03-28 04:19:46
Title	gabpa_gm12878
Description	chipseq of gabpa_gm12878
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}}
Peak caller	macs2

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2	ctl3
Total Reads	18449028	31154672	39044699	63956615	29995521
Total Reads (QC-failed)	0	0	0	0	0
Duplicate Reads	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0
Mapped Reads	15892463	27775708	37465805	48324826	28754388
Mapped Reads (QC-failed)	0	0	0	0	0
% Mapped Reads	86.1	89.2	96.0	75.6	95.89999999999999
Paired Reads	0	0	0	0	0
Paired Reads (QC-failed)	0	0	0	0	0
Read1	0	0	0	0	0
Read1 (QC-failed)	0	0	0	0	0
Read2	0	0	0	0	0
Read2 (QC-failed)	0	0	0	0	0
Properly Paired Reads	0	0	0	0	0
Properly Paired Reads (QC-failed)	0	0	0	0	0
% Properly Paired Reads	0.0	0.0	0.0	0.0	0.0
With itself	0	0	0	0	0
With itself (QC-failed)	0	0	0	0	0
Singletons	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0
Diff. Chroms (QC-failed)	0	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2	ctl3
Unpaired Reads	13848215	23188738	31754832	39568368	23413653
Paired Reads	0	0	0	0	0
Unmapped Reads	0	0	0	0	0
Unpaired Duplicate Reads	2180414	3038972	3884233	756470	3736718
Paired Duplicate Reads	0	0	0	0	0
Paired Optical Duplicate Reads	0	0	0	0	0
% Duplicate Reads	15.7451	13.1054	12.2319	1.9118	15.959599999999998

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
Total Reads	13848215	23188738	31754832	39568368	23413653
Total Reads (QC-failed)	0	0	0	0	0
Duplicate Reads	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0
Mapped Reads	13848215	23188738	31754832	39568368	23413653
Mapped Reads (QC-failed)	0	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0	100.0
Paired Reads	0	0	0	0	0
Paired Reads (QC-failed)	0	0	0	0	0
Read1	0	0	0	0	0
Read1 (QC-failed)	0	0	0	0	0
Read2	0	0	0	0	0
Read2 (QC-failed)	0	0	0	0	0
Properly Paired Reads	0	0	0	0	0
Properly Paired Reads (QC-failed)	0	0	0	0	0
% Properly Paired Reads	0.0	0.0	0.0	0.0	0.0
With itself	0	0	0	0	0
With itself (QC-failed)	0	0	0	0	0
Singletons	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0
Diff. Chroms (QC-failed)	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
Total Fragments	13769448	23158676	30718134	39359760	22499598
Distinct Fragments	11647484	20136773	27847275	38790858	19653021
Positions with Two Read	1158887	2039524	405892	430141	191124
NRF = Distinct/Total	0.845893	0.869513	0.906542	0.985546	0.873483
PBC1 = OneRead/Distinct	0.875753	0.881046	0.976158	0.987876	0.977996
PBC2 = OneRead/TwoRead	8.80182	8.698804	66.971857	89.08832	100.565999

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	16791	6132
N1	31392	8284
N2	13423	4897
Np	24000	9702
N optimal	24000	9702
N conservative	16791	6132
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.429337144899053	1.582191780821918
Self Consistency Ratio	2.338672427922223	1.6916479477230957
Reproducibility Test	borderline	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	178654	147079

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	100.0	130.0	115.0	115.0
25 percentile	100.0	130.0	243.0	169.0
50 percentile (median)	100.0	130.0	333.0	230.0
75 percentile	129.0	169.0	490.75	335.0
Max size	3246.0	3382.0	3379.0	3379.0
Mean	130.95711822853113	165.46277850678888	398.1468769325912	284.60333333333335

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	13769735	15000000
Estimated Fragment Length	100	130
Cross-correlation at Estimated Fragment Length	0.263082268506735	0.225880455980054
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.231983	0.1975409
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.1284662	0.1383429
NSC (Normalized Strand Cross-correlation coeff.)	2.047871	1.632758
RSC (Relative Strand Cross-correlation coeff.)	1.300428	1.478724

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	0.16189282101810068	0.23638575087207428
Synthetic AUC	0.4868296051207713	0.48975013390413985
X-intercept	0.30862153764950034	0.15820747511826075
Synthetic X-intercept	1.5485730169248656e-48	9.135516258405656e-81
Elbow Point	0.7282382249093301	0.6163433739998321
Synthetic Elbow Point	0.4935897799831345	0.5034671381038168
JS Distance	0.23268787561771054	0.24435125128837754
Synthetic JS Distance	0.4141273228676289	0.335390629839835
% Genome Enriched	41.42624648616659	53.41366666266799
Diff. Enrichment	16.93887647659657	10.403794914733833
CHANCE Divergence	0.18092302066614946	0.11599104638351118

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	0.21427389739399627	0.12519228083908662	0.25574543320237064	0.12055179544484051	0.2561456661487178	0.12066866252057357	0.13742442581602218	0.15164551598924686	0.15213184929472598

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	0.1075159449536791	0.15434400751288163	0.08247331096672876	0.11266458663594708

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	0.09395295017924396	0.12949625637672438	0.07265854657549713	0.10111803743682694

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