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Report generated at 2019-10-13 21:36:31

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	120347630	137158696
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	117653840	133265587
Mapped(QC-failed)	0	0
% Mapped	97.7600	97.1600
Paired	120347630	137158696
Paired(QC-failed)	0	0
Read1	60173815	68579348
Read1(QC-failed)	0	0
Read2	60173815	68579348
Read2(QC-failed)	0	0
Properly Paired	115839797	131002100
Properly Paired(QC-failed)	0	0
% Properly Paired	96.2500	95.5100
With itself	116207887	131535060
With itself(QC-failed)	0	0
Singletons	1445953	1730527
Singletons(QC-failed)	0	0
% Singleton	1.2000	1.2600
Diff. Chroms	116846	98144
Diff. Chroms (QC-failed)	0	0

Marking duplicates (filtered BAM)

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

	rep1	ctl1
Unpaired Reads	0	0
Paired Reads	50175299	54747675
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6291442	1493596
Paired Opt. Dupes	6518	7775
% Dupes/100	0.1254	0.0273

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	50172514	54683489
Distinct Read Pairs	43881371	53193120
One Read Pair	38365196	51758910
Two Read Pairs	4833757	1391528
NRF = Distinct/Total	0.8746	0.9727
PBC1 = OnePair/Distinct	0.8743	0.9730
PBC2 = OnePair/TwoPair	7.9369	37.1957

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	ctl1
Total	87767714	106508158
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	87767714	106508158
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	87767714	106508158
Paired(QC-failed)	0	0
Read1	43883857	53254079
Read1(QC-failed)	0	0
Read2	43883857	53254079
Read2(QC-failed)	0	0
Properly Paired	87767714	106508158
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	87767714	106508158
With itself(QC-failed)	0	0
Singletons	0	0
Singletons(QC-failed)	0	0
% Singleton	0.0000	0.0000
Diff. Chroms	0	0
Diff. Chroms (QC-failed)	0	0

Peak calling

Reproducibility QC and peak detection statistics

The number of peaks is capped at 300K for peak-caller MACS2

	overlap
Nt	0
N1	118415
Np	0
N optimal	118415
N conservative	118415
Optimal Set	rep1-pr
Conservative Set	rep1-pr
Rescue Ratio	0.0000
Self Consistency Ratio	1.0000
Reproducibility	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'

Enrichment

Strand cross-correlation measures

Performed on subsampled reads (15M)

	rep1
Reads	15000000
Est. Fragment Len.	200
Corr. Est. Fragment Len.	0.1804
Phantom Peak	50
Corr. Phantom Peak	0.1821
Argmin. Corr.	1500
Min. Corr.	0.1712
NSC	1.0535
RSC	0.8389

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-pr
Fraction of Reads in Peak	0.2307

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)

Other quality metrics

Fingerprint and Jensen-Shannon distance

	rep1
% genome enriched	0.2281
AUC	0.4956
CHANCE divergence	0.1247
Elbow Point	0.0000
JS Distance	0.6670
Synthetic AUC	0.4962
Synthetic Elbow Point	0.1663
Synthetic JS Distance	0.3606