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Report generated at 2021-10-09 18:08:30

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	122546796	168628396
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	116910942	163343908
Mapped(QC-failed)	0	0
% Mapped	95.4000	96.8700
Paired	122546796	168628396
Paired(QC-failed)	0	0
Read1	61273398	84314198
Read1(QC-failed)	0	0
Read2	61273398	84314198
Read2(QC-failed)	0	0
Properly Paired	114747157	159133434
Properly Paired(QC-failed)	0	0
% Properly Paired	93.6400	94.3700
With itself	116190777	162244869
With itself(QC-failed)	0	0
Singletons	720165	1099039
Singletons(QC-failed)	0	0
% Singleton	0.5900	0.6500
Diff. Chroms	963888	2067566
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	47835754	66322288
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3969486	4095947
Paired Opt. Dupes	39260	41316
% Dupes/100	0.0830	0.0618

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	47835519	66307420
Distinct Read Pairs	43866056	62212428
One Read Pair	40186925	58305094
Two Read Pairs	3409284	3728896
NRF = Distinct/Total	0.9170	0.9382
PBC1 = OnePair/Distinct	0.9161	0.9372
PBC2 = OnePair/TwoPair	11.7875	15.6360

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	87732536	124452682
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	87732536	124452682
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	87732536	124452682
Paired(QC-failed)	0	0
Read1	43866268	62226341
Read1(QC-failed)	0	0
Read2	43866268	62226341
Read2(QC-failed)	0	0
Properly Paired	87732536	124452682
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	87732536	124452682
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	132846
Np	0
N optimal	132846
N conservative	132846
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.	145
Corr. Est. Fragment Len.	0.1723
Phantom Peak	50
Corr. Phantom Peak	0.1777
Argmin. Corr.	1500
Min. Corr.	0.1689
NSC	1.0200
RSC	0.3835

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	0.1102

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	0.2626
AUC	0.4947
CHANCE divergence	0.1209
Elbow Point	0.0000
JS Distance	0.5862
Synthetic AUC	0.4981
Synthetic Elbow Point	0.1613
Synthetic JS Distance	0.2985