ENCSR936XTK (subsampled 1/67, chr19 and chrM Only)

ZNF143 ChIP-seq on human GM12878

Pipeline version: v1.1.8

Report generated at 2019-05-23 20:27:20

Paired-end: [True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True]

Pipeline type: TF ChIP-Seq

Genome: hg38_chr19_chrM_klab.tsv

Peak caller: SPP

Alignment

Flagstat (raw BAM)

	rep1 (PE)	rep2 (PE)	ctl1 (PE)	ctl2 (PE)
Total	1037412	1299678	1135028	1085984
Total(QC-failed)	0	0	0	0
Dupes	0	0	0	0
Dupes(QC-failed)	0	0	0	0
Mapped	85367	97977	81021	81878
Mapped(QC-failed)	0	0	0	0
% Mapped	8.2300	7.5400	7.1400	7.5400
Paired	1037412	1299678	1135028	1085984
Paired(QC-failed)	0	0	0	0
Read1	518706	649839	567514	542992
Read1(QC-failed)	0	0	0	0
Read2	518706	649839	567514	542992
Read2(QC-failed)	0	0	0	0
Properly Paired	69328	76347	59460	60740
Properly Paired(QC-failed)	0	0	0	0
% Properly Paired	6.6800	5.8700	5.2400	5.5900
With itself	73921	83141	64102	65497
With itself(QC-failed)	0	0	0	0
Singletons	11446	14836	16919	16381
Singletons(QC-failed)	0	0	0	0
% Singleton	1.1000	1.1400	1.4900	1.5100
Diff. Chroms	3	1	0	7
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	21408	20395	15345	16451
Unmapped Reads	0	0	0	0
Unpaired Dupes	0	0	0	0
Paired Dupes	57	39	31	44
Paired Opt. Dupes	0	0	0	0
% Dupes/100	0.0027	0.0019	0.0020	0.0027

Library complexity (filtered non-mito BAM)

	rep1 (PE)	rep2 (PE)	ctl1 (PE)	ctl2 (PE)
Total Reads (Pairs)	18123	18300	8674	9003
Distinct Reads (Pairs)	18072	18265	8662	8989
One Read (Pair)	18021	18230	8650	8976
Two Reads (Pairs)	51	35	12	12
NRF = Distinct/Total	0.9972	0.9981	0.9986	0.9984
PBC1 = OnePair/Distinct	0.9972	0.9981	0.9986	0.9986
PBC2 = OnePair/TwoPair	353.3529	520.8571	720.8333	748.0000

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	42702	40712	30628	32814
Total(QC-failed)	0	0	0	0
Dupes	0	0	0	0
Dupes(QC-failed)	0	0	0	0
Mapped	42702	40712	30628	32814
Mapped(QC-failed)	0	0	0	0
% Mapped	100.0000	100.0000	100.0000	100.0000
Paired	42702	40712	30628	32814
Paired(QC-failed)	0	0	0	0
Read1	21351	20356	15314	16407
Read1(QC-failed)	0	0	0	0
Read2	21351	20356	15314	16407
Read2(QC-failed)	0	0	0	0
Properly Paired	42702	40712	30628	32814
Properly Paired(QC-failed)	0	0	0	0
% Properly Paired	100.0000	100.0000	100.0000	100.0000
With itself	42702	40712	30628	32814
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	385	251
N1	282	133
N2	231	86
Np	379	246
N optimal	385	251
N conservative	385	251
Optimal Set	rep1-rep2	rep1-rep2
Conservative Set	rep1-rep2	rep1-rep2
Rescue Ratio	1.0158	1.0203
Self Consistency Ratio	1.2208	1.5465
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 (80K)

	rep1	rep2
Reads	64872	80996
Est. Fragment Len.	225	225
Corr. Est. Fragment Len.	0.0914	0.0876
Phantom Peak	50	50
Corr. Phantom Peak	0.1247	0.1560
Argmin. Corr.	1500	1500
Min. Corr.	0.0462	0.0612
NSC	1.9778	1.4302
RSC	0.5751	0.2780

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	0.3047	0.3453	0.2241	0.3033

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	0.2788	0.2634	0.1509	0.2758

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	0.0231	0.0348
AUC	0.4766	0.4760
CHANCE divergence	0.8799	0.8556
Elbow Point	0.0000	0.0000
JS Distance	0.8904	0.8677
Synthetic AUC	0.5151	0.4984
Synthetic Elbow Point	0.3431	0.3340
Synthetic JS Distance	0.4895	0.4052