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Report generated at 2021-10-10 06:58:08

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	97335914	215916580
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	94026585	212163850
Mapped(QC-failed)	0	0
% Mapped	96.6000	98.2600
Paired	97335914	215916580
Paired(QC-failed)	0	0
Read1	48667957	107958290
Read1(QC-failed)	0	0
Read2	48667957	107958290
Read2(QC-failed)	0	0
Properly Paired	92351026	203494730
Properly Paired(QC-failed)	0	0
% Properly Paired	94.8800	94.2500
With itself	93192570	210124486
With itself(QC-failed)	0	0
Singletons	834015	2039364
Singletons(QC-failed)	0	0
% Singleton	0.8600	0.9400
Diff. Chroms	539218	4820338
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	40496742	84863940
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	5381959	4207317
Paired Opt. Dupes	14920	26763
% Dupes/100	0.1329	0.0496

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	40488360	84737544
Distinct Read Pairs	35107449	80538942
One Read Pair	30339197	76496172
Two Read Pairs	4218397	3894193
NRF = Distinct/Total	0.8671	0.9505
PBC1 = OnePair/Distinct	0.8642	0.9498
PBC2 = OnePair/TwoPair	7.1921	19.6437

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	70229566	161313246
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	70229566	161313246
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	70229566	161313246
Paired(QC-failed)	0	0
Read1	35114783	80656623
Read1(QC-failed)	0	0
Read2	35114783	80656623
Read2(QC-failed)	0	0
Properly Paired	70229566	161313246
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	70229566	161313246
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	85603
Np	0
N optimal	85603
N conservative	85603
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.	205
Corr. Est. Fragment Len.	0.2221
Phantom Peak	50
Corr. Phantom Peak	0.2177
Argmin. Corr.	1500
Min. Corr.	0.1862
NSC	1.1932
RSC	1.1420

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	0.4622

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	0.1678
AUC	0.4941
CHANCE divergence	0.1311
Elbow Point	0.0000
JS Distance	0.8162
Synthetic AUC	0.5046
Synthetic Elbow Point	0.4045
Synthetic JS Distance	0.4813