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Report generated at 2020-07-10 13:39:37

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	178044380	139755050
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	166742900	137561007
Mapped(QC-failed)	0	0
% Mapped	93.6500	98.4300
Paired	178044380	139755050
Paired(QC-failed)	0	0
Read1	89022190	69877525
Read1(QC-failed)	0	0
Read2	89022190	69877525
Read2(QC-failed)	0	0
Properly Paired	161109155	132606533
Properly Paired(QC-failed)	0	0
% Properly Paired	90.4900	94.8800
With itself	165190843	136829005
With itself(QC-failed)	0	0
Singletons	1552057	732002
Singletons(QC-failed)	0	0
% Singleton	0.8700	0.5200
Diff. Chroms	310697	310461
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	62047457	58306381
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6696846	449204
Paired Opt. Dupes	4567	3926
% Dupes/100	0.1079	0.0077

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	62023471	58283535
Distinct Read Pairs	55330828	57836429
One Read Pair	49369157	57413097
Two Read Pairs	5401151	414907
NRF = Distinct/Total	0.8921	0.9923
PBC1 = OnePair/Distinct	0.8923	0.9927
PBC2 = OnePair/TwoPair	9.1405	138.3758

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	110701222	115714354
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	110701222	115714354
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	110701222	115714354
Paired(QC-failed)	0	0
Read1	55350611	57857177
Read1(QC-failed)	0	0
Read2	55350611	57857177
Read2(QC-failed)	0	0
Properly Paired	110701222	115714354
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	110701222	115714354
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	223619
Np	0
N optimal	223619
N conservative	223619
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.	135
Corr. Est. Fragment Len.	0.1861
Phantom Peak	50
Corr. Phantom Peak	0.2068
Argmin. Corr.	1500
Min. Corr.	0.1747
NSC	1.0651
RSC	0.3551

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	0.3389

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	0.2294
AUC	0.4961
CHANCE divergence	0.1015
Elbow Point	0.0000
JS Distance	0.7041
Synthetic AUC	0.5035
Synthetic Elbow Point	0.2401
Synthetic JS Distance	0.3666