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Report generated at 2019-10-26 09:11:35

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	84545698	265917970
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	79758361	247468185
Mapped(QC-failed)	0	0
% Mapped	94.3400	93.0600
Paired	84545698	265917970
Paired(QC-failed)	0	0
Read1	42272849	132958985
Read1(QC-failed)	0	0
Read2	42272849	132958985
Read2(QC-failed)	0	0
Properly Paired	75945136	230014508
Properly Paired(QC-failed)	0	0
% Properly Paired	89.8300	86.5000
With itself	76489531	235762666
With itself(QC-failed)	0	0
Singletons	3268830	11705519
Singletons(QC-failed)	0	0
% Singleton	3.8700	4.4000
Diff. Chroms	150925	1000428
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	31024649	94715746
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	14356440	28466270
Paired Opt. Dupes	2392	5233
% Dupes/100	0.4627	0.3005

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	31015270	94356916
Distinct Read Pairs	16663114	66005399
One Read Pair	8315442	44764253
Two Read Pairs	4601035	15674972
NRF = Distinct/Total	0.5373	0.6995
PBC1 = OnePair/Distinct	0.4990	0.6782
PBC2 = OnePair/TwoPair	1.8073	2.8558

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	33336418	132498952
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	33336418	132498952
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	33336418	132498952
Paired(QC-failed)	0	0
Read1	16668209	66249476
Read1(QC-failed)	0	0
Read2	16668209	66249476
Read2(QC-failed)	0	0
Properly Paired	33336418	132498952
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	33336418	132498952
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	46117
Np	0
N optimal	46117
N conservative	46117
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.	185
Corr. Est. Fragment Len.	0.1422
Phantom Peak	50
Corr. Phantom Peak	0.1403
Argmin. Corr.	1500
Min. Corr.	0.1221
NSC	1.1645
RSC	1.1063

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	0.2063

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	0.2169
AUC	0.4914
CHANCE divergence	0.1646
Elbow Point	0.0000
JS Distance	0.6760
Synthetic AUC	0.5139
Synthetic Elbow Point	0.2437
Synthetic JS Distance	0.3657