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Report generated at 2020-05-18 20:31:10

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	104609506	188531594
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	99122229	183497192
Mapped(QC-failed)	0	0
% Mapped	94.7500	97.3300
Paired	104609506	188531594
Paired(QC-failed)	0	0
Read1	52304753	94265797
Read1(QC-failed)	0	0
Read2	52304753	94265797
Read2(QC-failed)	0	0
Properly Paired	97542716	180692140
Properly Paired(QC-failed)	0	0
% Properly Paired	93.2400	95.8400
With itself	98447264	182539954
With itself(QC-failed)	0	0
Singletons	674965	957238
Singletons(QC-failed)	0	0
% Singleton	0.6500	0.5100
Diff. Chroms	453195	942066
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	42327343	78941456
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	255607	448927
Paired Opt. Dupes	1301	2929
% Dupes/100	0.0060	0.0057

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42322312	78883545
Distinct Read Pairs	42066747	78435677
One Read Pair	41812933	77991934
Two Read Pairs	252093	439949
NRF = Distinct/Total	0.9940	0.9943
PBC1 = OnePair/Distinct	0.9940	0.9943
PBC2 = OnePair/TwoPair	165.8631	177.2749

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	84143472	156985058
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84143472	156985058
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	84143472	156985058
Paired(QC-failed)	0	0
Read1	42071736	78492529
Read1(QC-failed)	0	0
Read2	42071736	78492529
Read2(QC-failed)	0	0
Properly Paired	84143472	156985058
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	84143472	156985058
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	105053
Np	0
N optimal	105053
N conservative	105053
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.	0.1844
Phantom Peak	50
Corr. Phantom Peak	0.2050
Argmin. Corr.	1500
Min. Corr.	0.1771
NSC	1.0408
RSC	0.2592

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	0.0767

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	0.2714
AUC	0.4956
CHANCE divergence	0.1071
Elbow Point	0.0000
JS Distance	0.5977
Synthetic AUC	0.5015
Synthetic Elbow Point	0.1027
Synthetic JS Distance	0.2910