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Report generated at 2019-10-25 20:37:40

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	128086672	152891984
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	126014064	151063238
Mapped(QC-failed)	0	0
% Mapped	98.3800	98.8000
Paired	128086672	152891984
Paired(QC-failed)	0	0
Read1	64043336	76445992
Read1(QC-failed)	0	0
Read2	64043336	76445992
Read2(QC-failed)	0	0
Properly Paired	123995499	148599864
Properly Paired(QC-failed)	0	0
% Properly Paired	96.8100	97.1900
With itself	125382798	150374699
With itself(QC-failed)	0	0
Singletons	631266	688539
Singletons(QC-failed)	0	0
% Singleton	0.4900	0.4500
Diff. Chroms	707226	759238
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	51955433	62318190
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1771500	1640545
Paired Opt. Dupes	19804	13302
% Dupes/100	0.0341	0.0263

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	51955265	62308524
Distinct Read Pairs	50183773	60668256
One Read Pair	48462001	59063633
Two Read Pairs	1673299	1570142
NRF = Distinct/Total	0.9659	0.9737
PBC1 = OnePair/Distinct	0.9657	0.9736
PBC2 = OnePair/TwoPair	28.9619	37.6167

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	100367866	121355290
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	100367866	121355290
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	100367866	121355290
Paired(QC-failed)	0	0
Read1	50183933	60677645
Read1(QC-failed)	0	0
Read2	50183933	60677645
Read2(QC-failed)	0	0
Properly Paired	100367866	121355290
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	100367866	121355290
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	114537
Np	0
N optimal	114537
N conservative	114537
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.	225
Corr. Est. Fragment Len.	0.1968
Phantom Peak	50
Corr. Phantom Peak	0.2064
Argmin. Corr.	1500
Min. Corr.	0.1901
NSC	1.0352
RSC	0.4097

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	0.3061

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	0.2100
AUC	0.4952
CHANCE divergence	0.1381
Elbow Point	0.0000
JS Distance	0.6670
Synthetic AUC	0.5040
Synthetic Elbow Point	0.2653
Synthetic JS Distance	0.3917