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Report generated at 2022-01-13 18:02:46

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	32771888	61483794
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	25036057	53537979
Mapped(QC-failed)	0	0
% Mapped	76.3900	87.0800
Paired	32771888	61483794
Paired(QC-failed)	0	0
Read1	16385944	30741897
Read1(QC-failed)	0	0
Read2	16385944	30741897
Read2(QC-failed)	0	0
Properly Paired	23884385	45512545
Properly Paired(QC-failed)	0	0
% Properly Paired	72.8800	74.0200
With itself	24103776	48321091
With itself(QC-failed)	0	0
Singletons	932281	5216888
Singletons(QC-failed)	0	0
% Singleton	2.8400	8.4800
Diff. Chroms	143970	1709831
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	10708996	7051123
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	152485	302597
Paired Opt. Dupes	1202	868
% Dupes/100	0.0142	0.0429

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	10708975	7050084
Distinct Read Pairs	10556490	6747724
One Read Pair	10406100	6457557
Two Read Pairs	148321	279052
NRF = Distinct/Total	0.9858	0.9571
PBC1 = OnePair/Distinct	0.9858	0.9570
PBC2 = OnePair/TwoPair	70.1593	23.1411

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	21113022	13497052
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	21113022	13497052
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	21113022	13497052
Paired(QC-failed)	0	0
Read1	10556511	6748526
Read1(QC-failed)	0	0
Read2	10556511	6748526
Read2(QC-failed)	0	0
Properly Paired	21113022	13497052
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	21113022	13497052
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	23972
Np	0
N optimal	23972
N conservative	23972
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 (12M)

	rep1
Reads	12836213
Est. Fragment Len.	235
Corr. Est. Fragment Len.	0.5853
Phantom Peak	55
Corr. Phantom Peak	0.4573
Argmin. Corr.	1500
Min. Corr.	0.1585
NSC	3.6915
RSC	1.4284

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	0.8266

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	0.0127
AUC	0.4909
CHANCE divergence	0.8002
Elbow Point	0.0000
JS Distance	0.9342
Synthetic AUC	0.5103
Synthetic Elbow Point	0.5833
Synthetic JS Distance	0.7395