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Report generated at 2020-07-10 02:19:51

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	118166608	150105716
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	116985521	148174218
Mapped(QC-failed)	0	0
% Mapped	99.0000	98.7100
Paired	118166608	150105716
Paired(QC-failed)	0	0
Read1	59083304	75052858
Read1(QC-failed)	0	0
Read2	59083304	75052858
Read2(QC-failed)	0	0
Properly Paired	116015248	145662973
Properly Paired(QC-failed)	0	0
% Properly Paired	98.1800	97.0400
With itself	116433225	147504283
With itself(QC-failed)	0	0
Singletons	552296	669935
Singletons(QC-failed)	0	0
% Singleton	0.4700	0.4500
Diff. Chroms	80052	160944
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	52777410	63945512
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	540795	447746
Paired Opt. Dupes	3467	2982
% Dupes/100	0.0102	0.0070

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	52639685	63774698
Distinct Read Pairs	52130109	63378830
One Read Pair	51629772	62997865
Two Read Pairs	493208	374780
NRF = Distinct/Total	0.9903	0.9938
PBC1 = OnePair/Distinct	0.9904	0.9940
PBC2 = OnePair/TwoPair	104.6815	168.0929

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	104473230	126995532
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	104473230	126995532
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	104473230	126995532
Paired(QC-failed)	0	0
Read1	52236615	63497766
Read1(QC-failed)	0	0
Read2	52236615	63497766
Read2(QC-failed)	0	0
Properly Paired	104473230	126995532
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	104473230	126995532
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	202264
Np	0
N optimal	202264
N conservative	202264
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.	150
Corr. Est. Fragment Len.	0.1760
Phantom Peak	50
Corr. Phantom Peak	0.1781
Argmin. Corr.	1500
Min. Corr.	0.1688
NSC	1.0427
RSC	0.7778

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	0.2787

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	0.2656
AUC	0.4960
CHANCE divergence	0.1023
Elbow Point	0.0000
JS Distance	0.6785
Synthetic AUC	0.5018
Synthetic Elbow Point	0.1841
Synthetic JS Distance	0.3065