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Report generated at 2019-10-31 17:18:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	122546414	258600350
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	120917341	255308360
Mapped(QC-failed)	0	0
% Mapped	98.6700	98.7300
Paired	122546414	258600350
Paired(QC-failed)	0	0
Read1	61273207	129300175
Read1(QC-failed)	0	0
Read2	61273207	129300175
Read2(QC-failed)	0	0
Properly Paired	119703165	246805576
Properly Paired(QC-failed)	0	0
% Properly Paired	97.6800	95.4400
With itself	120471750	253638863
With itself(QC-failed)	0	0
Singletons	445591	1669497
Singletons(QC-failed)	0	0
% Singleton	0.3600	0.6500
Diff. Chroms	170073	3939809
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	51216922	102636351
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	24299759	13145537
Paired Opt. Dupes	13091	27145
% Dupes/100	0.4744	0.1281

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	51215382	102579949
Distinct Read Pairs	26916331	89443009
One Read Pair	14108220	77822807
Two Read Pairs	6636529	10274703
NRF = Distinct/Total	0.5256	0.8719
PBC1 = OnePair/Distinct	0.5242	0.8701
PBC2 = OnePair/TwoPair	2.1258	7.5742

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	53834326	178981628
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53834326	178981628
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	53834326	178981628
Paired(QC-failed)	0	0
Read1	26917163	89490814
Read1(QC-failed)	0	0
Read2	26917163	89490814
Read2(QC-failed)	0	0
Properly Paired	53834326	178981628
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	53834326	178981628
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	139697
Np	0
N optimal	139697
N conservative	139697
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.	170
Corr. Est. Fragment Len.	0.1505
Phantom Peak	50
Corr. Phantom Peak	0.1525
Argmin. Corr.	1500
Min. Corr.	0.1402
NSC	1.0730
RSC	0.8324

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	0.3785

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	0.1906
AUC	0.4932
CHANCE divergence	0.1550
Elbow Point	0.0000
JS Distance	0.7388
Synthetic AUC	0.5003
Synthetic Elbow Point	0.3239
Synthetic JS Distance	0.4152