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Report generated at 2022-01-13 08:39:47

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	50557058	39854584
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	45000617	37062784
Mapped(QC-failed)	0	0
% Mapped	89.0100	93.0000
Paired	50557058	39854584
Paired(QC-failed)	0	0
Read1	25278529	19927292
Read1(QC-failed)	0	0
Read2	25278529	19927292
Read2(QC-failed)	0	0
Properly Paired	42564168	33407063
Properly Paired(QC-failed)	0	0
% Properly Paired	84.1900	83.8200
With itself	43766638	35838648
With itself(QC-failed)	0	0
Singletons	1233979	1224136
Singletons(QC-failed)	0	0
% Singleton	2.4400	3.0700
Diff. Chroms	322708	1658864
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	15511271	13479178
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	155508	344808
Paired Opt. Dupes	8898	7792
% Dupes/100	0.0100	0.0256

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	15510334	13471162
Distinct Read Pairs	15354836	13126691
One Read Pair	15200985	12789814
Two Read Pairs	152258	329426
NRF = Distinct/Total	0.9900	0.9744
PBC1 = OnePair/Distinct	0.9900	0.9743
PBC2 = OnePair/TwoPair	99.8370	38.8245

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	30711526	26268740
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	30711526	26268740
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	30711526	26268740
Paired(QC-failed)	0	0
Read1	15355763	13134370
Read1(QC-failed)	0	0
Read2	15355763	13134370
Read2(QC-failed)	0	0
Properly Paired	30711526	26268740
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	30711526	26268740
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	145994
Np	0
N optimal	145994
N conservative	145994
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.	235
Corr. Est. Fragment Len.	0.2135
Phantom Peak	50
Corr. Phantom Peak	0.2565
Argmin. Corr.	1500
Min. Corr.	0.1995
NSC	1.0701
RSC	0.2453

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	0.2579

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	0.1616
AUC	0.4926
CHANCE divergence	0.2812
Elbow Point	0.0000
JS Distance	0.7097
Synthetic AUC	0.5005
Synthetic Elbow Point	0.1224
Synthetic JS Distance	0.4055