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Report generated at 2020-05-18 11:51:55

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	83236808	137038710
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78276554	132965142
Mapped(QC-failed)	0	0
% Mapped	94.0400	97.0300
Paired	83236808	137038710
Paired(QC-failed)	0	0
Read1	41618404	68519355
Read1(QC-failed)	0	0
Read2	41618404	68519355
Read2(QC-failed)	0	0
Properly Paired	77518095	130403765
Properly Paired(QC-failed)	0	0
% Properly Paired	93.1300	95.1600
With itself	77922338	132147488
With itself(QC-failed)	0	0
Singletons	354216	817654
Singletons(QC-failed)	0	0
% Singleton	0.4300	0.6000
Diff. Chroms	177839	1017994
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	34806714	56489373
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	291584	246609
Paired Opt. Dupes	1216	1947
% Dupes/100	0.0084	0.0044

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34800021	56440954
Distinct Read Pairs	34508502	56195118
One Read Pair	34219302	55950441
Two Read Pairs	286906	243541
NRF = Distinct/Total	0.9916	0.9956
PBC1 = OnePair/Distinct	0.9916	0.9956
PBC2 = OnePair/TwoPair	119.2701	229.7373

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	69030260	112485528
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	69030260	112485528
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	69030260	112485528
Paired(QC-failed)	0	0
Read1	34515130	56242764
Read1(QC-failed)	0	0
Read2	34515130	56242764
Read2(QC-failed)	0	0
Properly Paired	69030260	112485528
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	69030260	112485528
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	31937
Np	0
N optimal	31937
N conservative	31937
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.	190
Corr. Est. Fragment Len.	0.2669
Phantom Peak	50
Corr. Phantom Peak	0.2639
Argmin. Corr.	1500
Min. Corr.	0.1804
NSC	1.4790
RSC	1.0351

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	0.3414

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	0.2102
AUC	0.4951
CHANCE divergence	0.1096
Elbow Point	0.0000
JS Distance	0.7704
Synthetic AUC	0.5085
Synthetic Elbow Point	0.3366
Synthetic JS Distance	0.4403