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Report generated at 2020-05-26 00:47:43

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	54834348	78085830
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	54259942	76610347
Mapped(QC-failed)	0	0
% Mapped	98.9500	98.1100
Paired	54834348	78085830
Paired(QC-failed)	0	0
Read1	27417174	39042915
Read1(QC-failed)	0	0
Read2	27417174	39042915
Read2(QC-failed)	0	0
Properly Paired	53845143	74378590
Properly Paired(QC-failed)	0	0
% Properly Paired	98.2000	95.2500
With itself	53935026	75950585
With itself(QC-failed)	0	0
Singletons	324916	659762
Singletons(QC-failed)	0	0
% Singleton	0.5900	0.8400
Diff. Chroms	13045	90080
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	25291558	32826215
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	678393	205201
Paired Opt. Dupes	2206	1517
% Dupes/100	0.0268	0.0063

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	25277492	32750640
Distinct Read Pairs	24600329	32567543
One Read Pair	23943412	32390569
Two Read Pairs	638462	174492
NRF = Distinct/Total	0.9732	0.9944
PBC1 = OnePair/Distinct	0.9733	0.9946
PBC2 = OnePair/TwoPair	37.5017	185.6278

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	49226330	65242028
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	49226330	65242028
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	49226330	65242028
Paired(QC-failed)	0	0
Read1	24613165	32621014
Read1(QC-failed)	0	0
Read2	24613165	32621014
Read2(QC-failed)	0	0
Properly Paired	49226330	65242028
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	49226330	65242028
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	115796
Np	0
N optimal	115796
N conservative	115796
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.	0.2043
Phantom Peak	45
Corr. Phantom Peak	0.1906
Argmin. Corr.	1500
Min. Corr.	0.1802
NSC	1.1333
RSC	2.3178

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	0.4331

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	0.1579
AUC	0.4942
CHANCE divergence	0.1885
Elbow Point	0.0000
JS Distance	0.7671
Synthetic AUC	0.4961
Synthetic Elbow Point	0.3351
Synthetic JS Distance	0.4668