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Report generated at 2020-05-02 11:16:49

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	38420512	62419198
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	28457103	59332552
Mapped(QC-failed)	0	0
% Mapped	74.0700	95.0500
Paired	38420512	62419198
Paired(QC-failed)	0	0
Read1	19210256	31209599
Read1(QC-failed)	0	0
Read2	19210256	31209599
Read2(QC-failed)	0	0
Properly Paired	26190563	52461075
Properly Paired(QC-failed)	0	0
% Properly Paired	68.1700	84.0500
With itself	27304029	57668835
With itself(QC-failed)	0	0
Singletons	1153074	1663717
Singletons(QC-failed)	0	0
% Singleton	3.0000	2.6700
Diff. Chroms	862515	3447428
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	11690061	21847540
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	306615	249487
Paired Opt. Dupes	1004	2578
% Dupes/100	0.0262	0.0114

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	11685229	21831865
Distinct Read Pairs	11378744	21582817
One Read Pair	11078835	21336142
Two Read Pairs	293459	244317
NRF = Distinct/Total	0.9738	0.9886
PBC1 = OnePair/Distinct	0.9736	0.9886
PBC2 = OnePair/TwoPair	37.7526	87.3297

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	22766892	43196106
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	22766892	43196106
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	22766892	43196106
Paired(QC-failed)	0	0
Read1	11383446	21598053
Read1(QC-failed)	0	0
Read2	11383446	21598053
Read2(QC-failed)	0	0
Properly Paired	22766892	43196106
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	22766892	43196106
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	43407
Np	0
N optimal	43407
N conservative	43407
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 (13M)

	rep1
Reads	13694316
Est. Fragment Len.	235
Corr. Est. Fragment Len.	0.2577
Phantom Peak	50
Corr. Phantom Peak	0.2418
Argmin. Corr.	1500
Min. Corr.	0.1759
NSC	1.4652
RSC	1.2410

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	0.3969

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	0.1031
AUC	0.4914
CHANCE divergence	0.4209
Elbow Point	0.0000
JS Distance	0.7736
Synthetic AUC	0.4942
Synthetic Elbow Point	0.3236
Synthetic JS Distance	0.4969