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Pipeline version: v1.1.7

Report generated at 2019-10-12 20:44:34

Paired-end: False

Pipeline type: TF ChIP-Seq

Genome: hg19_klab.tsv

Peak caller: SPP

Alignment

Flagstat (raw BAM)

	rep1	rep2	ctl1
Total	15329142	63707371	57444550
Total(QC-failed)	0	0	0
Dupes	0	0	0
Dupes(QC-failed)	0	0	0
Mapped	14113187	40459957	34552286
Mapped(QC-failed)	0	0	0
% Mapped	92.0700	63.5100	60.1500
Paired	0	0	0
Paired(QC-failed)	0	0	0
Read1	0	0	0
Read1(QC-failed)	0	0	0
Read2	0	0	0
Read2(QC-failed)	0	0	0
Properly Paired	0	0	0
Properly Paired(QC-failed)	0	0	0
% Properly Paired	0.0000	0.0000	0.0000
With itself	0	0	0
With itself(QC-failed)	0	0	0
Singletons	0	0	0
Singletons(QC-failed)	0	0	0
% Singleton	0.0000	0.0000	0.0000
Diff. Chroms	0	0	0
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

Filtered out (samtools view -F 1804):

read unmapped (0x4)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

	rep1	rep2	ctl1
Unpaired Reads	11029140	27509959	22975627
Paired Reads	0	0	0
Unmapped Reads	0	0	0
Unpaired Dupes	830862	20051012	206977
Paired Dupes	0	0	0
Paired Opt. Dupes	0	0	0
% Dupes/100	0.0753	0.7289	0.0090

Library complexity (filtered non-mito BAM)

	rep1	rep2	ctl1
Total Reads	11006084	27447905	22886568
Distinct Reads	10222781	9424583	22788081
One Read	9529239	3311257	22701124
Two Reads	646486	1884730	83850
NRF = Distinct/Total	0.9288	0.3434	0.9957
PBC1 = OneRead/Distinct	0.9322	0.3513	0.9962
PBC2 = OneRead/TwoReads	14.7401	1.7569	270.7349

Mitochondrial reads are filtered out.

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

Flagstat (filtered/deduped BAM)

Filtered and duplicates removed

	rep1	rep2	ctl1
Total	10198278	7458947	22768650
Total(QC-failed)	0	0	0
Dupes	0	0	0
Dupes(QC-failed)	0	0	0
Mapped	10198278	7458947	22768650
Mapped(QC-failed)	0	0	0
% Mapped	100.0000	100.0000	100.0000
Paired	0	0	0
Paired(QC-failed)	0	0	0
Read1	0	0	0
Read1(QC-failed)	0	0	0
Read2	0	0	0
Read2(QC-failed)	0	0	0
Properly Paired	0	0	0
Properly Paired(QC-failed)	0	0	0
% Properly Paired	0.0000	0.0000	0.0000
With itself	0	0	0
With itself(QC-failed)	0	0	0
Singletons	0	0	0
Singletons(QC-failed)	0	0	0
% Singleton	0.0000	0.0000	0.0000
Diff. Chroms	0	0	0
Diff. Chroms (QC-failed)	0	0	0

Peak calling

IDR (Irreproducible Discovery Rate) plots

Reproducibility QC and peak detection statistics

The number of peaks is capped at 300K for peak-caller SPP

	overlap	IDR
Nt	37268	5581
N1	10218	2624
N2	23994	3795
Np	46376	8435
N optimal	46376	8435
N conservative	37268	5581
Optimal Set	ppr	ppr
Conservative Set	rep1-rep2	rep1-rep2
Rescue Ratio	1.2444	1.5114
Self Consistency Ratio	2.3482	1.4463
Reproducibility	borderline	pass

Overlapping peaks

N1: Replicate 1 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Nt: True Replicate consisten overlapping peaks (comparing true replicates Rep1 vs Rep2 )
Np: Pooled-pseudoreplicate consistent overlapping 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'

IDR (Irreproducible Discovery Rate) peaks

N1: Replicate 1 self-consistent IDR 0.05 peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent IDR 0.05 peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Nt: True Replicate consistent IDR 0.05 peaks (comparing true replicates Rep1 vs Rep2 )
Np: Pooled-pseudoreplicate consistent IDR 0.05 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'

Enrichment

Strand cross-correlation measures

Performed on subsampled reads (14M)

	rep1	rep2
Reads	14073677	15000000
Est. Fragment Len.	105	120
Corr. Est. Fragment Len.	0.1598	0.1112
Phantom Peak	35	35
Corr. Phantom Peak	0.1709	0.1030
Argmin. Corr.	1500	1500
Min. Corr.	0.1437	0.0816
NSC	1.1120	1.3623
RSC	0.5907	1.3858

NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.

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

Fraction of reads in overlapping peaks

	rep1-rep2	rep1-pr	rep2-pr	ppr
Fraction of Reads in Peak	0.0472	0.0187	0.0562	0.0548

ppr: Overlapping peaks comparing pooled pseudo replicates
rep1-pr: Overlapping peaks comparing pseudoreplicates from replicate 1
rep2-pr: Overlapping peaks comparing pseudoreplicates from replicate 2
repi-repj: Overlapping peaks comparing true replicates (rep i vs. rep j)

Fraction of reads in IDR peaks

	rep1-rep2	rep1-pr	rep2-pr	ppr
Fraction of Reads in Peak	0.0183	0.0097	0.0207	0.0230

ppr: IDR peaks comparing pooled pseudo replicates
rep1-pr: IDR peaks comparing pseudoreplicates from replicate 1
rep2-pr: IDR peaks comparing pseudoreplicates from replicate 2
repi-repj: IDR peaks comparing true replicates (rep i vs. rep j)

Other quality metrics

Fingerprint and Jensen-Shannon distance

	rep1	rep2
% genome enriched	0.2233	0.1428
AUC	0.4816	0.4785
CHANCE divergence	0.3022	0.4937
Elbow Point	0.0000	0.0000
JS Distance	0.5716	0.7255
Synthetic AUC	0.4851	0.4815
Synthetic Elbow Point	0.0860	0.1494
Synthetic JS Distance	0.2302	0.2871