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Report generated at 2019-10-13 05:24:13

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	111486788	112182380
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	108149991	109790255
Mapped(QC-failed)	0	0
% Mapped	97.0100	97.8700
Paired	111486788	112182380
Paired(QC-failed)	0	0
Read1	55743394	56091190
Read1(QC-failed)	0	0
Read2	55743394	56091190
Read2(QC-failed)	0	0
Properly Paired	107121970	108525037
Properly Paired(QC-failed)	0	0
% Properly Paired	96.0800	96.7400
With itself	107543688	109236441
With itself(QC-failed)	0	0
Singletons	606303	553814
Singletons(QC-failed)	0	0
% Singleton	0.5400	0.4900
Diff. Chroms	118462	375641
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	47064452	47985507
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	14560852	3406633
Paired Opt. Dupes	6521	6387
% Dupes/100	0.3094	0.0710

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	47063328	47950820
Distinct Read Pairs	32502815	44546891
One Read Pair	22478366	41387028
Two Read Pairs	6871278	2937039
NRF = Distinct/Total	0.6906	0.9290
PBC1 = OnePair/Distinct	0.6916	0.9291
PBC2 = OnePair/TwoPair	3.2714	14.0914

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	65007200	89157748
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	65007200	89157748
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	65007200	89157748
Paired(QC-failed)	0	0
Read1	32503600	44578874
Read1(QC-failed)	0	0
Read2	32503600	44578874
Read2(QC-failed)	0	0
Properly Paired	65007200	89157748
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	65007200	89157748
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	38179
Np	0
N optimal	38179
N conservative	38179
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.	120
Corr. Est. Fragment Len.	0.1607
Phantom Peak	50
Corr. Phantom Peak	0.1711
Argmin. Corr.	1500
Min. Corr.	0.1541
NSC	1.0433
RSC	0.3919

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	0.0502

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	0.3095
AUC	0.4949
CHANCE divergence	0.1030
Elbow Point	0.0000
JS Distance	0.5363
Synthetic AUC	0.5066
Synthetic Elbow Point	0.0688
Synthetic JS Distance	0.2334