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Report generated at 2020-05-13 06:40:28

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	57539974	55554290
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53307314	53234328
Mapped(QC-failed)	0	0
% Mapped	92.6400	95.8200
Paired	57539974	55554290
Paired(QC-failed)	0	0
Read1	28769987	27777145
Read1(QC-failed)	0	0
Read2	28769987	27777145
Read2(QC-failed)	0	0
Properly Paired	51016563	46813080
Properly Paired(QC-failed)	0	0
% Properly Paired	88.6600	84.2700
With itself	52278574	52018273
With itself(QC-failed)	0	0
Singletons	1028740	1216055
Singletons(QC-failed)	0	0
% Singleton	1.7900	2.1900
Diff. Chroms	911137	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	23108340	19892586
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	358065	222592
Paired Opt. Dupes	2716	2281
% Dupes/100	0.0155	0.0112

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	23107422	19890387
Distinct Read Pairs	22749370	19667823
One Read Pair	22396209	19447434
Two Read Pairs	348335	218233
NRF = Distinct/Total	0.9845	0.9888
PBC1 = OnePair/Distinct	0.9845	0.9888
PBC2 = OnePair/TwoPair	64.2950	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	45500550	39339988
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	45500550	39339988
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	45500550	39339988
Paired(QC-failed)	0	0
Read1	22750275	19669994
Read1(QC-failed)	0	0
Read2	22750275	19669994
Read2(QC-failed)	0	0
Properly Paired	45500550	39339988
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	45500550	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	25757
Np	0
N optimal	25757
N conservative	25757
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.	295
Corr. Est. Fragment Len.	0.3399
Phantom Peak	55
Corr. Phantom Peak	0.2883
Argmin. Corr.	1500
Min. Corr.	0.1811
NSC	1.8767
RSC	1.4822

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	0.4234

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	0.1125
AUC	0.4939
CHANCE divergence	0.3763
Elbow Point	0.0000
JS Distance	0.7418
Synthetic AUC	0.5092
Synthetic Elbow Point	0.3801
Synthetic JS Distance	0.5172