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Report generated at 2019-10-12 20:45:11

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	70732760	115682520
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	61709950	110134967
Mapped(QC-failed)	0	0
% Mapped	87.2400	95.2000
Paired	70732760	115682520
Paired(QC-failed)	0	0
Read1	35366380	57841260
Read1(QC-failed)	0	0
Read2	35366380	57841260
Read2(QC-failed)	0	0
Properly Paired	57422991	104877577
Properly Paired(QC-failed)	0	0
% Properly Paired	81.1800	90.6600
With itself	57819972	106096677
With itself(QC-failed)	0	0
Singletons	3889978	4038290
Singletons(QC-failed)	0	0
% Singleton	5.5000	3.4900
Diff. Chroms	246915	752647
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	23224536	44143515
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	19649952	1315729
Paired Opt. Dupes	2291	4867
% Dupes/100	0.8461	0.0298

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	23223884	44113008
Distinct Read Pairs	3574462	42798457
One Read Pair	511264	41528318
Two Read Pairs	437861	1233455
NRF = Distinct/Total	0.1539	0.9702
PBC1 = OnePair/Distinct	0.1430	0.9703
PBC2 = OnePair/TwoPair	1.1676	33.6683

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	7149168	85655572
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	7149168	85655572
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	7149168	85655572
Paired(QC-failed)	0	0
Read1	3574584	42827786
Read1(QC-failed)	0	0
Read2	3574584	42827786
Read2(QC-failed)	0	0
Properly Paired	7149168	85655572
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	7149168	85655572
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	52757
Np	0
N optimal	52757
N conservative	52757
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.	0.0648
Phantom Peak	50
Corr. Phantom Peak	0.0565
Argmin. Corr.	1500
Min. Corr.	0.0450
NSC	1.4407
RSC	1.7280

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	0.3583

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	0.0838
AUC	0.4847
CHANCE divergence	0.6437
Elbow Point	0.0000
JS Distance	0.7299
Synthetic AUC	0.5014
Synthetic Elbow Point	0.3042
Synthetic JS Distance	0.3993