ENCSR936XTK

ZNF143 ChIP-seq on human GM12878

Pipeline version: v1.2.2

Report generated at 2019-07-14 07:50:04

Paired-end: [True, True]

Pipeline type: TF ChIP-Seq

Genome: hg38_google.tsv

Peak caller: SPP

Alignment

Flagstat (raw BAM)

	rep1 (PE)	rep2 (PE)	ctl1 (PE)	ctl2 (PE)
Total	69122852	86590386	90753054	86825372
Total(QC-failed)	0	0	0	0
Dupes	0	0	0	0
Dupes(QC-failed)	0	0	0	0
Mapped	68063712	83658387	89164565	85203319
Mapped(QC-failed)	0	0	0	0
% Mapped	98.4700	96.6100	98.2500	98.1300
Paired	69122852	86590386	90753054	86825372
Paired(QC-failed)	0	0	0	0
Read1	34561426	43295193	45376527	43412686
Read1(QC-failed)	0	0	0	0
Read2	34561426	43295193	45376527	43412686
Read2(QC-failed)	0	0	0	0
Properly Paired	67691510	83126958	88383742	84455733
Properly Paired(QC-failed)	0	0	0	0
% Properly Paired	97.9300	96.0000	97.3900	97.2700
With itself	67846541	83375973	88810063	84838815
With itself(QC-failed)	0	0	0	0
Singletons	217171	282414	354502	364504
Singletons(QC-failed)	0	0	0	0
% Singleton	0.3100	0.3300	0.3900	0.4200
Diff. Chroms	28970	44892	123377	113675
Diff. Chroms (QC-failed)	0	0	0	0

Marking duplicates (filtered BAM)

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)

	rep1 (PE)	rep2 (PE)	ctl1 (PE)	ctl2 (PE)
Unpaired Reads	0	0	0	0
Paired Reads	30291259	37072602	39854681	38118550
Unmapped Reads	0	0	0	0
Unpaired Dupes	0	0	0	0
Paired Dupes	3664057	2833119	4092825	4128511
Paired Opt. Dupes	8743	24855	8937	8553
% Dupes/100	0.1210	0.0764	0.1027	0.1083

Library complexity (filtered non-mito BAM)

	rep1 (PE)	rep2 (PE)	ctl1 (PE)	ctl2 (PE)
Total Reads (Pairs)	30099108	36950601	39400720	37604471
Distinct Reads (Pairs)	26466206	34130627	35389661	33580171
One Read (Pair)	23226034	31510426	31987615	29976868
Two Reads (Pairs)	2888067	2434584	2993615	3230526
NRF = Distinct/Total	0.8793	0.9237	0.8982	0.8930
PBC1 = OnePair/Distinct	0.8776	0.9232	0.9039	0.8927
PBC2 = OnePair/TwoPair	8.0421	12.9428	10.6853	9.2793

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 (PE)	rep2 (PE)	ctl1 (PE)	ctl2 (PE)
Total	53254404	68478966	71523712	67980078
Total(QC-failed)	0	0	0	0
Dupes	0	0	0	0
Dupes(QC-failed)	0	0	0	0
Mapped	53254404	68478966	71523712	67980078
Mapped(QC-failed)	0	0	0	0
% Mapped	100.0000	100.0000	100.0000	100.0000
Paired	53254404	68478966	71523712	67980078
Paired(QC-failed)	0	0	0	0
Read1	26627202	34239483	35761856	33990039
Read1(QC-failed)	0	0	0	0
Read2	26627202	34239483	35761856	33990039
Read2(QC-failed)	0	0	0	0
Properly Paired	53254404	68478966	71523712	67980078
Properly Paired(QC-failed)	0	0	0	0
% Properly Paired	100.0000	100.0000	100.0000	100.0000
With itself	53254404	68478966	71523712	67980078
With itself(QC-failed)	0	0	0	0
Singletons	0	0	0	0
Singletons(QC-failed)	0	0	0	0
% Singleton	0.0000	0.0000	0.0000	0.0000
Diff. Chroms	0	0	0	0
Diff. Chroms (QC-failed)	0	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	94395	27396
N1	83370	20968
N2	66706	13849
Np	97950	29253
N optimal	97950	29253
N conservative	94395	27396
Optimal Set	ppr	ppr
Conservative Set	rep1-rep2	rep1-rep2
Rescue Ratio	1.0377	1.0678
Self Consistency Ratio	1.2498	1.5140
Reproducibility	pass	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 (15M)

	rep1	rep2
Reads	15000000	15000000
Est. Fragment Len.	225	210
Corr. Est. Fragment Len.	0.2550	0.2380
Phantom Peak	50	50
Corr. Phantom Peak	0.2034	0.2127
Argmin. Corr.	1500	1500
Min. Corr.	0.1469	0.1699
NSC	1.7358	1.4009
RSC	1.9130	1.5900

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	0.1312	0.1584	0.0955	0.1332

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	0.0929	0.1119	0.0612	0.0947

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	0.2531	0.2828
AUC	0.4952	0.4958
CHANCE divergence	0.1090	0.1003
Elbow Point	0.0000	0.0000
JS Distance	0.6581	0.6163
Synthetic AUC	0.5074	0.5049
Synthetic Elbow Point	0.2181	0.1719
Synthetic JS Distance	0.3517	0.3033