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Report generated at 2019-10-12 18:28:18

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	71662862	70427534
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	66365686	69036340
Mapped(QC-failed)	0	0
% Mapped	92.6100	98.0200
Paired	71662862	70427534
Paired(QC-failed)	0	0
Read1	35831431	35213767
Read1(QC-failed)	0	0
Read2	35831431	35213767
Read2(QC-failed)	0	0
Properly Paired	65861591	68456801
Properly Paired(QC-failed)	0	0
% Properly Paired	91.9000	97.2000
With itself	66078550	68728853
With itself(QC-failed)	0	0
Singletons	287136	307487
Singletons(QC-failed)	0	0
% Singleton	0.4000	0.4400
Diff. Chroms	31234	67653
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	30085307	30027609
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	9868167	502205
Paired Opt. Dupes	4844	5522
% Dupes/100	0.3280	0.0167

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	30073174	29867632
Distinct Read Pairs	20208909	29376965
One Read Pair	13316679	28893133
Two Read Pairs	4748727	477131
NRF = Distinct/Total	0.6720	0.9836
PBC1 = OnePair/Distinct	0.6590	0.9835
PBC2 = OnePair/TwoPair	2.8043	60.5560

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	40434280	59050808
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	40434280	59050808
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	40434280	59050808
Paired(QC-failed)	0	0
Read1	20217140	29525404
Read1(QC-failed)	0	0
Read2	20217140	29525404
Read2(QC-failed)	0	0
Properly Paired	40434280	59050808
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	40434280	59050808
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	48846
Np	0
N optimal	48846
N conservative	48846
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.	190
Corr. Est. Fragment Len.	0.3642
Phantom Peak	55
Corr. Phantom Peak	0.3089
Argmin. Corr.	1500
Min. Corr.	0.1701
NSC	2.1403
RSC	1.3987

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	0.5509

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	0.1129
AUC	0.4936
CHANCE divergence	0.2409
Elbow Point	0.0000
JS Distance	0.8713
Synthetic AUC	0.5075
Synthetic Elbow Point	0.4988
Synthetic JS Distance	0.5783