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Report generated at 2020-05-13 08:00:51

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	50413742	55554290
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	43552426	53234328
Mapped(QC-failed)	0	0
% Mapped	86.3900	95.8200
Paired	50413742	55554290
Paired(QC-failed)	0	0
Read1	25206871	27777145
Read1(QC-failed)	0	0
Read2	25206871	27777145
Read2(QC-failed)	0	0
Properly Paired	38865583	46813080
Properly Paired(QC-failed)	0	0
% Properly Paired	77.0900	84.2700
With itself	41857758	52018273
With itself(QC-failed)	0	0
Singletons	1694668	1216055
Singletons(QC-failed)	0	0
% Singleton	3.3600	2.1900
Diff. Chroms	1060894	3541644
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	15426486	19892586
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	162613	222592
Paired Opt. Dupes	1987	2281
% Dupes/100	0.0105	0.0112

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	15426097	19890387
Distinct Read Pairs	15263486	19667823
One Read Pair	15102346	19447434
Two Read Pairs	159695	218233
NRF = Distinct/Total	0.9895	0.9888
PBC1 = OnePair/Distinct	0.9894	0.9888
PBC2 = OnePair/TwoPair	94.5699	89.1132

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	30527746	39339988
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	30527746	39339988
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	30527746	39339988
Paired(QC-failed)	0	0
Read1	15263873	19669994
Read1(QC-failed)	0	0
Read2	15263873	19669994
Read2(QC-failed)	0	0
Properly Paired	30527746	39339988
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	30527746	39339988
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	87834
Np	0
N optimal	87834
N conservative	87834
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.	285
Corr. Est. Fragment Len.	0.2077
Phantom Peak	50
Corr. Phantom Peak	0.2328
Argmin. Corr.	1500
Min. Corr.	0.1841
NSC	1.1284
RSC	0.4852

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	0.1737

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	0.1587
AUC	0.4926
CHANCE divergence	0.3854
Elbow Point	0.0000
JS Distance	0.6517
Synthetic AUC	0.4971
Synthetic Elbow Point	0.1027
Synthetic JS Distance	0.3581