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Report generated at 2020-05-26 21:59:12

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	141779094	199901914
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	140519244	196913276
Mapped(QC-failed)	0	0
% Mapped	99.1100	98.5000
Paired	141779094	199901914
Paired(QC-failed)	0	0
Read1	70889547	99950957
Read1(QC-failed)	0	0
Read2	70889547	99950957
Read2(QC-failed)	0	0
Properly Paired	139710151	192680093
Properly Paired(QC-failed)	0	0
% Properly Paired	98.5400	96.3900
With itself	139846476	195797647
With itself(QC-failed)	0	0
Singletons	672768	1115629
Singletons(QC-failed)	0	0
% Singleton	0.4700	0.5600
Diff. Chroms	35104	160902
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	64521340	85640559
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2135302	851284
Paired Opt. Dupes	6373	5480
% Dupes/100	0.0331	0.0099

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	64504182	85585893
Distinct Read Pairs	62369822	84745487
One Read Pair	60324760	83939401
Two Read Pairs	1964206	790418
NRF = Distinct/Total	0.9669	0.9902
PBC1 = OnePair/Distinct	0.9672	0.9905
PBC2 = OnePair/TwoPair	30.7120	106.1962

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	124772076	169578550
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	124772076	169578550
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	124772076	169578550
Paired(QC-failed)	0	0
Read1	62386038	84789275
Read1(QC-failed)	0	0
Read2	62386038	84789275
Read2(QC-failed)	0	0
Properly Paired	124772076	169578550
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	124772076	169578550
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	126709
Np	0
N optimal	126709
N conservative	126709
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.	0.2091
Phantom Peak	45
Corr. Phantom Peak	0.1946
Argmin. Corr.	1500
Min. Corr.	0.1811
NSC	1.1547
RSC	2.0669

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	0.5694

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	0.1489
AUC	0.4964
CHANCE divergence	0.1091
Elbow Point	0.0000
JS Distance	0.8305
Synthetic AUC	0.4972
Synthetic Elbow Point	0.4185
Synthetic JS Distance	0.5222