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Report generated at 2021-02-06 02:08:22

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	118813652	120623008
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	118124752	118852959
Mapped(QC-failed)	0	0
% Mapped	99.4200	98.5300
Paired	118813652	120623008
Paired(QC-failed)	0	0
Read1	59406826	60311504
Read1(QC-failed)	0	0
Read2	59406826	60311504
Read2(QC-failed)	0	0
Properly Paired	116071647	116324482
Properly Paired(QC-failed)	0	0
% Properly Paired	97.6900	96.4400
With itself	117739205	118246914
With itself(QC-failed)	0	0
Singletons	385547	606045
Singletons(QC-failed)	0	0
% Singleton	0.3200	0.5000
Diff. Chroms	63269	142153
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	54644688	50494792
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	682613	383179
Paired Opt. Dupes	45922	18017
% Dupes/100	0.0125	0.0076

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	54629400	50475444
Distinct Read Pairs	53947435	50093864
One Read Pair	53283344	49738212
Two Read Pairs	647354	346479
NRF = Distinct/Total	0.9875	0.9924
PBC1 = OnePair/Distinct	0.9877	0.9929
PBC2 = OnePair/TwoPair	82.3094	143.5533

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	107924150	100223226
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	107924150	100223226
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	107924150	100223226
Paired(QC-failed)	0	0
Read1	53962075	50111613
Read1(QC-failed)	0	0
Read2	53962075	50111613
Read2(QC-failed)	0	0
Properly Paired	107924150	100223226
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	107924150	100223226
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	268027
Np	0
N optimal	268027
N conservative	268027
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.	0.1995
Phantom Peak	55
Corr. Phantom Peak	0.1881
Argmin. Corr.	1500
Min. Corr.	0.1719
NSC	1.1609
RSC	1.7084

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	0.5802

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	0.1412
AUC	0.4960
CHANCE divergence	0.1527
Elbow Point	0.0000
JS Distance	0.7876
Synthetic AUC	0.5053
Synthetic Elbow Point	0.3563
Synthetic JS Distance	0.5134