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Report generated at 2019-11-01 01:30:39

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	79965190	317909612
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78362825	312072580
Mapped(QC-failed)	0	0
% Mapped	98.0000	98.1600
Paired	79965190	317909612
Paired(QC-failed)	0	0
Read1	39982595	158954806
Read1(QC-failed)	0	0
Read2	39982595	158954806
Read2(QC-failed)	0	0
Properly Paired	76802118	294728580
Properly Paired(QC-failed)	0	0
% Properly Paired	96.0400	92.7100
With itself	77940414	309884253
With itself(QC-failed)	0	0
Singletons	422411	2188327
Singletons(QC-failed)	0	0
% Singleton	0.5300	0.6900
Diff. Chroms	474584	9012143
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	31518317	121497414
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	14832228	13623598
Paired Opt. Dupes	11210	34172
% Dupes/100	0.4706	0.1121

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	31513925	121417759
Distinct Read Pairs	16683676	107806572
One Read Pair	8313904	95829671
Two Read Pairs	4508035	10543184
NRF = Distinct/Total	0.5294	0.8879
PBC1 = OnePair/Distinct	0.4983	0.8889
PBC2 = OnePair/TwoPair	1.8442	9.0893

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	33372178	215747632
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	33372178	215747632
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	33372178	215747632
Paired(QC-failed)	0	0
Read1	16686089	107873816
Read1(QC-failed)	0	0
Read2	16686089	107873816
Read2(QC-failed)	0	0
Properly Paired	33372178	215747632
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	33372178	215747632
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	55249
Np	0
N optimal	55249
N conservative	55249
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.	125
Corr. Est. Fragment Len.	0.1238
Phantom Peak	50
Corr. Phantom Peak	0.1325
Argmin. Corr.	1500
Min. Corr.	0.1199
NSC	1.0329
RSC	0.3123

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	0.0385

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	0.2793
AUC	0.4914
CHANCE divergence	0.1468
Elbow Point	0.0000
JS Distance	0.5559
Synthetic AUC	0.4937
Synthetic Elbow Point	0.1440
Synthetic JS Distance	0.2452