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Report generated at 2020-07-10 03:08:53

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	63893556	166164986
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	60609102	163647560
Mapped(QC-failed)	0	0
% Mapped	94.8600	98.4800
Paired	63893556	166164986
Paired(QC-failed)	0	0
Read1	31946778	83082493
Read1(QC-failed)	0	0
Read2	31946778	83082493
Read2(QC-failed)	0	0
Properly Paired	60135754	159369723
Properly Paired(QC-failed)	0	0
% Properly Paired	94.1200	95.9100
With itself	60400956	162885733
With itself(QC-failed)	0	0
Singletons	208146	761827
Singletons(QC-failed)	0	0
% Singleton	0.3300	0.4600
Diff. Chroms	21505	172110
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	27820041	70155381
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2249608	564841
Paired Opt. Dupes	1700	3752
% Dupes/100	0.0809	0.0081

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	27812315	70119762
Distinct Read Pairs	25563401	69558647
One Read Pair	23496348	69027662
Two Read Pairs	1911450	519769
NRF = Distinct/Total	0.9191	0.9920
PBC1 = OnePair/Distinct	0.9191	0.9924
PBC2 = OnePair/TwoPair	12.2924	132.8045

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	51140866	139181080
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	51140866	139181080
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	51140866	139181080
Paired(QC-failed)	0	0
Read1	25570433	69590540
Read1(QC-failed)	0	0
Read2	25570433	69590540
Read2(QC-failed)	0	0
Properly Paired	51140866	139181080
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	51140866	139181080
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	117846
Np	0
N optimal	117846
N conservative	117846
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.	150
Corr. Est. Fragment Len.	0.1991
Phantom Peak	55
Corr. Phantom Peak	0.1766
Argmin. Corr.	1500
Min. Corr.	0.1618
NSC	1.2306
RSC	2.5090

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	0.3493

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	0.1957
AUC	0.4943
CHANCE divergence	0.1423
Elbow Point	0.0000
JS Distance	0.7413
Synthetic AUC	0.4948
Synthetic Elbow Point	0.3206
Synthetic JS Distance	0.4176