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Report generated at 2022-09-03 18:33:03

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	162268944	137088680
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	149557018	134896264
Mapped(QC-failed)	0	0
% Mapped	92.1700	98.4000
Paired	162268944	137088680
Paired(QC-failed)	0	0
Read1	81134472	68544340
Read1(QC-failed)	0	0
Read2	81134472	68544340
Read2(QC-failed)	0	0
Properly Paired	146317648	134028989
Properly Paired(QC-failed)	0	0
% Properly Paired	90.1700	97.7700
With itself	147634946	134480082
With itself(QC-failed)	0	0
Singletons	1922072	416182
Singletons(QC-failed)	0	0
% Singleton	1.1800	0.3000
Diff. Chroms	194985	105917
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	51962928	59008108
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3092024	3208268
Paired Opt. Dupes	7038	16913
% Dupes/100	0.0595	0.0544

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	51962170	58974886
Distinct Read Pairs	48870189	55768361
One Read Pair	45990723	52823522
Two Read Pairs	2702152	2707860
NRF = Distinct/Total	0.9405	0.9456
PBC1 = OnePair/Distinct	0.9411	0.9472
PBC2 = OnePair/TwoPair	17.0200	19.5075

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	97741808	111599680
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	97741808	111599680
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	97741808	111599680
Paired(QC-failed)	0	0
Read1	48870904	55799840
Read1(QC-failed)	0	0
Read2	48870904	55799840
Read2(QC-failed)	0	0
Properly Paired	97741808	111599680
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	97741808	111599680
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	220949
Np	0
N optimal	220949
N conservative	220949
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.	110
Corr. Est. Fragment Len.	0.2168
Phantom Peak	50
Corr. Phantom Peak	0.2660
Argmin. Corr.	1500
Min. Corr.	0.2043
NSC	1.0612
RSC	0.2025

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	0.2747

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	0.2147
AUC	0.4959
CHANCE divergence	0.1207
Elbow Point	0.0000
JS Distance	0.6540
Synthetic AUC	0.5029
Synthetic Elbow Point	0.2323
Synthetic JS Distance	0.3859