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Report generated at 2020-05-20 17:46:40

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	118741092	136790320
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	116679571	132380851
Mapped(QC-failed)	0	0
% Mapped	98.2600	96.7800
Paired	118741092	136790320
Paired(QC-failed)	0	0
Read1	59370546	68395160
Read1(QC-failed)	0	0
Read2	59370546	68395160
Read2(QC-failed)	0	0
Properly Paired	115380425	130092484
Properly Paired(QC-failed)	0	0
% Properly Paired	97.1700	95.1000
With itself	116359744	131677058
With itself(QC-failed)	0	0
Singletons	319827	703793
Singletons(QC-failed)	0	0
% Singleton	0.2700	0.5100
Diff. Chroms	586635	604160
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	53010883	56350303
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	290797	241110
Paired Opt. Dupes	2015	2032
% Dupes/100	0.0055	0.0043

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	53008259	56321306
Distinct Read Pairs	52717481	56080639
One Read Pair	52427994	55842177
Two Read Pairs	288203	236573
NRF = Distinct/Total	0.9945	0.9957
PBC1 = OnePair/Distinct	0.9945	0.9957
PBC2 = OnePair/TwoPair	181.9134	236.0463

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	105440172	112218386
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	105440172	112218386
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	105440172	112218386
Paired(QC-failed)	0	0
Read1	52720086	56109193
Read1(QC-failed)	0	0
Read2	52720086	56109193
Read2(QC-failed)	0	0
Properly Paired	105440172	112218386
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	105440172	112218386
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	256500
Np	0
N optimal	256500
N conservative	256500
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.	125
Corr. Est. Fragment Len.	0.1974
Phantom Peak	50
Corr. Phantom Peak	0.1988
Argmin. Corr.	1500
Min. Corr.	0.1793
NSC	1.1010
RSC	0.9327

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	0.3470

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	0.1856
AUC	0.4960
CHANCE divergence	0.1452
Elbow Point	0.0000
JS Distance	0.7073
Synthetic AUC	0.5011
Synthetic Elbow Point	0.1993
Synthetic JS Distance	0.4293