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Report generated at 2020-06-10 22:50:03

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	141804700	134911976
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	133147190	131561748
Mapped(QC-failed)	0	0
% Mapped	93.8900	97.5200
Paired	141804700	134911976
Paired(QC-failed)	0	0
Read1	70902350	67455988
Read1(QC-failed)	0	0
Read2	70902350	67455988
Read2(QC-failed)	0	0
Properly Paired	131011526	129326575
Properly Paired(QC-failed)	0	0
% Properly Paired	92.3900	95.8600
With itself	132313347	130892790
With itself(QC-failed)	0	0
Singletons	833843	668958
Singletons(QC-failed)	0	0
% Singleton	0.5900	0.5000
Diff. Chroms	717201	887686
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	57831270	56597685
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	376482	240684
Paired Opt. Dupes	1443	1949
% Dupes/100	0.0065	0.0043

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	57826207	56554078
Distinct Read Pairs	57449771	56313956
One Read Pair	57076129	56074958
Two Read Pairs	370870	237897
NRF = Distinct/Total	0.9935	0.9958
PBC1 = OnePair/Distinct	0.9935	0.9958
PBC2 = OnePair/TwoPair	153.8979	235.7111

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	114909576	112714002
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	114909576	112714002
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	114909576	112714002
Paired(QC-failed)	0	0
Read1	57454788	56357001
Read1(QC-failed)	0	0
Read2	57454788	56357001
Read2(QC-failed)	0	0
Properly Paired	114909576	112714002
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	114909576	112714002
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	214391
Np	0
N optimal	214391
N conservative	214391
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.	145
Corr. Est. Fragment Len.	0.1879
Phantom Peak	50
Corr. Phantom Peak	0.2028
Argmin. Corr.	1500
Min. Corr.	0.1794
NSC	1.0479
RSC	0.3671

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	0.3099

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	0.2336
AUC	0.4962
CHANCE divergence	0.1036
Elbow Point	0.0000
JS Distance	0.7010
Synthetic AUC	0.4998
Synthetic Elbow Point	0.2020
Synthetic JS Distance	0.3605