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Report generated at 2020-06-05 22:47:11

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	143238978	65794820
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	136828396	63417692
Mapped(QC-failed)	0	0
% Mapped	95.5200	96.3900
Paired	143238978	65794820
Paired(QC-failed)	0	0
Read1	71619489	32897410
Read1(QC-failed)	0	0
Read2	71619489	32897410
Read2(QC-failed)	0	0
Properly Paired	133213098	61746812
Properly Paired(QC-failed)	0	0
% Properly Paired	93.0000	93.8500
With itself	134002974	61970109
With itself(QC-failed)	0	0
Singletons	2825422	1447583
Singletons(QC-failed)	0	0
% Singleton	1.9700	2.2000
Diff. Chroms	135190	55379
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	54093574	26833523
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	5082789	435866
Paired Opt. Dupes	3346	1445
% Dupes/100	0.0940	0.0162

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	54092953	26817652
Distinct Read Pairs	49010228	26382149
One Read Pair	44332307	25952967
Two Read Pairs	4302292	422975
NRF = Distinct/Total	0.9060	0.9838
PBC1 = OnePair/Distinct	0.9046	0.9837
PBC2 = OnePair/TwoPair	10.3043	61.3582

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	98021570	52795314
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	98021570	52795314
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	98021570	52795314
Paired(QC-failed)	0	0
Read1	49010785	26397657
Read1(QC-failed)	0	0
Read2	49010785	26397657
Read2(QC-failed)	0	0
Properly Paired	98021570	52795314
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	98021570	52795314
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	70206
Np	0
N optimal	70206
N conservative	70206
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.	120
Corr. Est. Fragment Len.	0.1850
Phantom Peak	50
Corr. Phantom Peak	0.2145
Argmin. Corr.	1500
Min. Corr.	0.1786
NSC	1.0359
RSC	0.1786

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	0.0310

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	0.2961
AUC	0.4959
CHANCE divergence	0.1004
Elbow Point	0.0000
JS Distance	0.5557
Synthetic AUC	0.5057
Synthetic Elbow Point	0.0577
Synthetic JS Distance	0.2555