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Report generated at 2020-05-20 17:26:19

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	115992370	202360194
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	115494569	199280518
Mapped(QC-failed)	0	0
% Mapped	99.5700	98.4800
Paired	115992370	202360194
Paired(QC-failed)	0	0
Read1	57996185	101180097
Read1(QC-failed)	0	0
Read2	57996185	101180097
Read2(QC-failed)	0	0
Properly Paired	115184763	196010642
Properly Paired(QC-failed)	0	0
% Properly Paired	99.3000	96.8600
With itself	115262511	198492948
With itself(QC-failed)	0	0
Singletons	232058	787570
Singletons(QC-failed)	0	0
% Singleton	0.2000	0.3900
Diff. Chroms	29030	212946
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	54355441	87251527
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	892096	1128860
Paired Opt. Dupes	4828	5289
% Dupes/100	0.0164	0.0129

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	54347947	87198629
Distinct Read Pairs	53456157	86085041
One Read Pair	52590029	85022082
Two Read Pairs	842546	1031715
NRF = Distinct/Total	0.9836	0.9872
PBC1 = OnePair/Distinct	0.9838	0.9877
PBC2 = OnePair/TwoPair	62.4180	82.4085

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	106926690	172245334
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	106926690	172245334
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	106926690	172245334
Paired(QC-failed)	0	0
Read1	53463345	86122667
Read1(QC-failed)	0	0
Read2	53463345	86122667
Read2(QC-failed)	0	0
Properly Paired	106926690	172245334
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	106926690	172245334
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	233943
Np	0
N optimal	233943
N conservative	233943
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.	160
Corr. Est. Fragment Len.	0.1967
Phantom Peak	55
Corr. Phantom Peak	0.1863
Argmin. Corr.	1500
Min. Corr.	0.1737
NSC	1.1323
RSC	1.8383

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	0.5901

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	0.1373
AUC	0.4961
CHANCE divergence	0.1638
Elbow Point	0.0000
JS Distance	0.7699
Synthetic AUC	0.4981
Synthetic Elbow Point	0.3663
Synthetic JS Distance	0.5177