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Report generated at 2019-11-03 14:07:52

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	127702506	155278814
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	126551926	152204810
Mapped(QC-failed)	0	0
% Mapped	99.1000	98.0200
Paired	127702506	155278814
Paired(QC-failed)	0	0
Read1	63851253	77639407
Read1(QC-failed)	0	0
Read2	63851253	77639407
Read2(QC-failed)	0	0
Properly Paired	125131029	149315055
Properly Paired(QC-failed)	0	0
% Properly Paired	97.9900	96.1600
With itself	125986793	151298295
With itself(QC-failed)	0	0
Singletons	565133	906515
Singletons(QC-failed)	0	0
% Singleton	0.4400	0.5800
Diff. Chroms	435863	1045401
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	57288820	66029859
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2188158	1524871
Paired Opt. Dupes	13163	14661
% Dupes/100	0.0382	0.0231

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	57288312	65968445
Distinct Read Pairs	55100173	64445697
One Read Pair	52975023	62945345
Two Read Pairs	2064017	1479272
NRF = Distinct/Total	0.9618	0.9769
PBC1 = OnePair/Distinct	0.9614	0.9767
PBC2 = OnePair/TwoPair	25.6660	42.5516

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	110201324	129009976
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	110201324	129009976
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	110201324	129009976
Paired(QC-failed)	0	0
Read1	55100662	64504988
Read1(QC-failed)	0	0
Read2	55100662	64504988
Read2(QC-failed)	0	0
Properly Paired	110201324	129009976
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	110201324	129009976
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	216509
Np	0
N optimal	216509
N conservative	216509
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.	185
Corr. Est. Fragment Len.	0.1781
Phantom Peak	50
Corr. Phantom Peak	0.1803
Argmin. Corr.	1500
Min. Corr.	0.1768
NSC	1.0075
RSC	0.3877

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	0.4299

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	0.2028
AUC	0.4961
CHANCE divergence	0.1152
Elbow Point	0.0000
JS Distance	0.6879
Synthetic AUC	0.4991
Synthetic Elbow Point	0.2864
Synthetic JS Distance	0.4071