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Report generated at 2020-05-31 03:17:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	145394868	196505800
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	143719398	193483775
Mapped(QC-failed)	0	0
% Mapped	98.8500	98.4600
Paired	145394868	196505800
Paired(QC-failed)	0	0
Read1	72697434	98252900
Read1(QC-failed)	0	0
Read2	72697434	98252900
Read2(QC-failed)	0	0
Properly Paired	142615396	182597399
Properly Paired(QC-failed)	0	0
% Properly Paired	98.0900	92.9200
With itself	142957705	192397679
With itself(QC-failed)	0	0
Singletons	761693	1086096
Singletons(QC-failed)	0	0
% Singleton	0.5200	0.5500
Diff. Chroms	50309	243413
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	63402084	81193783
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2491130	858603
Paired Opt. Dupes	3943	4308
% Dupes/100	0.0393	0.0106

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	63399081	81187332
Distinct Read Pairs	60908122	80329098
One Read Pair	58513478	79518226
Two Read Pairs	2306565	792113
NRF = Distinct/Total	0.9607	0.9894
PBC1 = OnePair/Distinct	0.9607	0.9899
PBC2 = OnePair/TwoPair	25.3682	100.3875

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	121821908	160670360
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	121821908	160670360
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	121821908	160670360
Paired(QC-failed)	0	0
Read1	60910954	80335180
Read1(QC-failed)	0	0
Read2	60910954	80335180
Read2(QC-failed)	0	0
Properly Paired	121821908	160670360
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	121821908	160670360
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	228527
Np	0
N optimal	228527
N conservative	228527
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.	0.1865
Phantom Peak	50
Corr. Phantom Peak	0.1874
Argmin. Corr.	1500
Min. Corr.	0.1794
NSC	1.0395
RSC	0.8917

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	0.2881

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	0.2148
AUC	0.4963
CHANCE divergence	0.1470
Elbow Point	0.0000
JS Distance	0.6213
Synthetic AUC	0.5029
Synthetic Elbow Point	0.2284
Synthetic JS Distance	0.3803