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Report generated at 2021-03-20 08:06:01

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	142212008	147967716
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	139472193	141073415
Mapped(QC-failed)	0	0
% Mapped	98.0700	95.3400
Paired	142212008	147967716
Paired(QC-failed)	0	0
Read1	71106004	73983858
Read1(QC-failed)	0	0
Read2	71106004	73983858
Read2(QC-failed)	0	0
Properly Paired	130356098	129978073
Properly Paired(QC-failed)	0	0
% Properly Paired	91.6600	87.8400
With itself	138523634	139642816
With itself(QC-failed)	0	0
Singletons	948559	1430599
Singletons(QC-failed)	0	0
% Singleton	0.6700	0.9700
Diff. Chroms	3277389	4101665
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	59071836	58170389
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4207534	1433825
Paired Opt. Dupes	3845	3355
% Dupes/100	0.0712	0.0246

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	59047851	58124153
Distinct Read Pairs	54843728	56701457
One Read Pair	50901172	55332829
Two Read Pairs	3704101	1333630
NRF = Distinct/Total	0.9288	0.9755
PBC1 = OnePair/Distinct	0.9281	0.9759
PBC2 = OnePair/TwoPair	13.7418	41.4904

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	109728604	113473128
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	109728604	113473128
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	109728604	113473128
Paired(QC-failed)	0	0
Read1	54864302	56736564
Read1(QC-failed)	0	0
Read2	54864302	56736564
Read2(QC-failed)	0	0
Properly Paired	109728604	113473128
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	109728604	113473128
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	168131
Np	0
N optimal	168131
N conservative	168131
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.	0.1735
Phantom Peak	50
Corr. Phantom Peak	0.1715
Argmin. Corr.	1500
Min. Corr.	0.1673
NSC	1.0371
RSC	1.4768

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	0.1905

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	0.2570
AUC	0.4961
CHANCE divergence	0.1067
Elbow Point	0.0000
JS Distance	0.6060
Synthetic AUC	0.5029
Synthetic Elbow Point	0.1665
Synthetic JS Distance	0.3188