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Report generated at 2020-06-06 02:00:30

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	115244044	121920692
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	110805281	119191863
Mapped(QC-failed)	0	0
% Mapped	96.1500	97.7600
Paired	115244044	121920692
Paired(QC-failed)	0	0
Read1	57622022	60960346
Read1(QC-failed)	0	0
Read2	57622022	60960346
Read2(QC-failed)	0	0
Properly Paired	109574060	117754194
Properly Paired(QC-failed)	0	0
% Properly Paired	95.0800	96.5800
With itself	109973790	118308645
With itself(QC-failed)	0	0
Singletons	831491	883218
Singletons(QC-failed)	0	0
% Singleton	0.7200	0.7200
Diff. Chroms	122190	122186
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	49705121	50862870
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	8070035	879406
Paired Opt. Dupes	6982	8068
% Dupes/100	0.1624	0.0173

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49703193	50817650
Distinct Read Pairs	41633422	49939924
One Read Pair	34856394	49088463
Two Read Pairs	5683189	832695
NRF = Distinct/Total	0.8376	0.9827
PBC1 = OnePair/Distinct	0.8372	0.9829
PBC2 = OnePair/TwoPair	6.1332	58.9513

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	83270172	99966928
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	83270172	99966928
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	83270172	99966928
Paired(QC-failed)	0	0
Read1	41635086	49983464
Read1(QC-failed)	0	0
Read2	41635086	49983464
Read2(QC-failed)	0	0
Properly Paired	83270172	99966928
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	83270172	99966928
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	134008
Np	0
N optimal	134008
N conservative	134008
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.	180
Corr. Est. Fragment Len.	0.1770
Phantom Peak	50
Corr. Phantom Peak	0.1769
Argmin. Corr.	1500
Min. Corr.	0.1670
NSC	1.0596
RSC	1.0052

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	0.2231

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	0.2337
AUC	0.4955
CHANCE divergence	0.1218
Elbow Point	0.0000
JS Distance	0.6598
Synthetic AUC	0.5071
Synthetic Elbow Point	0.1584
Synthetic JS Distance	0.3521