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Report generated at 2019-10-27 02:56:24

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	116015740	340975906
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	114446724	331955873
Mapped(QC-failed)	0	0
% Mapped	98.6500	97.3500
Paired	116015740	340975906
Paired(QC-failed)	0	0
Read1	58007870	170487953
Read1(QC-failed)	0	0
Read2	58007870	170487953
Read2(QC-failed)	0	0
Properly Paired	112805035	317967837
Properly Paired(QC-failed)	0	0
% Properly Paired	97.2300	93.2500
With itself	113940156	329465448
With itself(QC-failed)	0	0
Singletons	506568	2490425
Singletons(QC-failed)	0	0
% Singleton	0.4400	0.7300
Diff. Chroms	271075	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	47718793	131944073
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	8368951	6909853
Paired Opt. Dupes	16964	32973
% Dupes/100	0.1754	0.0524

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	47710965	131852916
Distinct Read Pairs	39343428	124951324
One Read Pair	32313024	118429996
Two Read Pairs	5886823	6176361
NRF = Distinct/Total	0.8246	0.9477
PBC1 = OnePair/Distinct	0.8213	0.9478
PBC2 = OnePair/TwoPair	5.4890	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	78699684	250068440
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78699684	250068440
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	78699684	250068440
Paired(QC-failed)	0	0
Read1	39349842	125034220
Read1(QC-failed)	0	0
Read2	39349842	125034220
Read2(QC-failed)	0	0
Properly Paired	78699684	250068440
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	78699684	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	160806
Np	0
N optimal	160806
N conservative	160806
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.	165
Corr. Est. Fragment Len.	0.1748
Phantom Peak	50
Corr. Phantom Peak	0.1781
Argmin. Corr.	1500
Min. Corr.	0.1706
NSC	1.0247
RSC	0.5607

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	0.3996

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	0.2050
AUC	0.4944
CHANCE divergence	0.1228
Elbow Point	0.0000
JS Distance	0.7552
Synthetic AUC	0.4979
Synthetic Elbow Point	0.3198
Synthetic JS Distance	0.4008