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Report generated at 2019-11-03 16:34:17

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	130509670	149933526
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	128819213	146624545
Mapped(QC-failed)	0	0
% Mapped	98.7000	97.7900
Paired	130509670	149933526
Paired(QC-failed)	0	0
Read1	65254835	74966763
Read1(QC-failed)	0	0
Read2	65254835	74966763
Read2(QC-failed)	0	0
Properly Paired	126918410	143525972
Properly Paired(QC-failed)	0	0
% Properly Paired	97.2500	95.7300
With itself	128175622	145761822
With itself(QC-failed)	0	0
Singletons	643591	862723
Singletons(QC-failed)	0	0
% Singleton	0.4900	0.5800
Diff. Chroms	377725	564786
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	57336355	63655918
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	838694	1138162
Paired Opt. Dupes	22408	22681
% Dupes/100	0.0146	0.0179

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	57336054	63588650
Distinct Read Pairs	56497363	62452487
One Read Pair	55667520	61334967
Two Read Pairs	821073	1100229
NRF = Distinct/Total	0.9854	0.9821
PBC1 = OnePair/Distinct	0.9853	0.9821
PBC2 = OnePair/TwoPair	67.7985	55.7475

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	112995322	125035512
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	112995322	125035512
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	112995322	125035512
Paired(QC-failed)	0	0
Read1	56497661	62517756
Read1(QC-failed)	0	0
Read2	56497661	62517756
Read2(QC-failed)	0	0
Properly Paired	112995322	125035512
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	112995322	125035512
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	197294
Np	0
N optimal	197294
N conservative	197294
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.	145
Corr. Est. Fragment Len.	0.1732
Phantom Peak	50
Corr. Phantom Peak	0.1742
Argmin. Corr.	1500
Min. Corr.	0.1719
NSC	1.0075
RSC	0.5500

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	0.1780

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	0.2619
AUC	0.4962
CHANCE divergence	0.1195
Elbow Point	0.0000
JS Distance	0.5815
Synthetic AUC	0.5045
Synthetic Elbow Point	0.1774
Synthetic JS Distance	0.3065