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Report generated at 2019-10-12 14:49:36

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	59961376	70427534
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	57708881	69036340
Mapped(QC-failed)	0	0
% Mapped	96.2400	98.0200
Paired	59961376	70427534
Paired(QC-failed)	0	0
Read1	29980688	35213767
Read1(QC-failed)	0	0
Read2	29980688	35213767
Read2(QC-failed)	0	0
Properly Paired	57448477	68456801
Properly Paired(QC-failed)	0	0
% Properly Paired	95.8100	97.2000
With itself	57539222	68728853
With itself(QC-failed)	0	0
Singletons	169659	307487
Singletons(QC-failed)	0	0
% Singleton	0.2800	0.4400
Diff. Chroms	25473	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	26863312	30027609
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1167664	502205
Paired Opt. Dupes	5197	5522
% Dupes/100	0.0435	0.0167

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	26859152	29867632
Distinct Read Pairs	25691713	29376965
One Read Pair	24569870	28893133
Two Read Pairs	1077857	477131
NRF = Distinct/Total	0.9565	0.9836
PBC1 = OnePair/Distinct	0.9563	0.9835
PBC2 = OnePair/TwoPair	22.7951	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	51391296	59050808
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	51391296	59050808
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	51391296	59050808
Paired(QC-failed)	0	0
Read1	25695648	29525404
Read1(QC-failed)	0	0
Read2	25695648	29525404
Read2(QC-failed)	0	0
Properly Paired	51391296	59050808
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	51391296	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	173264
Np	0
N optimal	173264
N conservative	173264
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.	180
Corr. Est. Fragment Len.	0.2122
Phantom Peak	55
Corr. Phantom Peak	0.2019
Argmin. Corr.	1500
Min. Corr.	0.1794
NSC	1.1826
RSC	1.4561

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	0.3897

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	0.1585
AUC	0.4943
CHANCE divergence	0.2204
Elbow Point	0.0000
JS Distance	0.7384
Synthetic AUC	0.4954
Synthetic Elbow Point	0.3157
Synthetic JS Distance	0.4505