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Report generated at 2019-10-27 05:12:46

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	109413078	340975906
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	107477924	331955873
Mapped(QC-failed)	0	0
% Mapped	98.2300	97.3500
Paired	109413078	340975906
Paired(QC-failed)	0	0
Read1	54706539	170487953
Read1(QC-failed)	0	0
Read2	54706539	170487953
Read2(QC-failed)	0	0
Properly Paired	106006925	317967837
Properly Paired(QC-failed)	0	0
% Properly Paired	96.8900	93.2500
With itself	106998553	329465448
With itself(QC-failed)	0	0
Singletons	479371	2490425
Singletons(QC-failed)	0	0
% Singleton	0.4400	0.7300
Diff. Chroms	169247	4791736
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	45232650	131944073
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	23276187	6909853
Paired Opt. Dupes	14055	32973
% Dupes/100	0.5146	0.0524

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	45222929	131852916
Distinct Read Pairs	21951635	124951324
One Read Pair	10237118	118429996
Two Read Pairs	5621314	6176361
NRF = Distinct/Total	0.4854	0.9477
PBC1 = OnePair/Distinct	0.4663	0.9478
PBC2 = OnePair/TwoPair	1.8211	19.1747

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	43912926	250068440
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	43912926	250068440
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	43912926	250068440
Paired(QC-failed)	0	0
Read1	21956463	125034220
Read1(QC-failed)	0	0
Read2	21956463	125034220
Read2(QC-failed)	0	0
Properly Paired	43912926	250068440
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	43912926	250068440
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	116712
Np	0
N optimal	116712
N conservative	116712
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.	155
Corr. Est. Fragment Len.	0.1332
Phantom Peak	50
Corr. Phantom Peak	0.1369
Argmin. Corr.	1500
Min. Corr.	0.1269
NSC	1.0495
RSC	0.6257

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	0.2613

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	0.2267
AUC	0.4925
CHANCE divergence	0.1469
Elbow Point	0.0000
JS Distance	0.6812
Synthetic AUC	0.5077
Synthetic Elbow Point	0.2691
Synthetic JS Distance	0.3495