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Report generated at 2020-07-14 18:29:42

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	94857852	61218190
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	88433247	56551430
Mapped(QC-failed)	0	0
% Mapped	93.2300	92.3800
Paired	94857852	61218190
Paired(QC-failed)	0	0
Read1	47428926	30609095
Read1(QC-failed)	0	0
Read2	47428926	30609095
Read2(QC-failed)	0	0
Properly Paired	84816146	43003222
Properly Paired(QC-failed)	0	0
% Properly Paired	89.4100	70.2500
With itself	86917343	54252500
With itself(QC-failed)	0	0
Singletons	1515904	2298930
Singletons(QC-failed)	0	0
% Singleton	1.6000	3.7600
Diff. Chroms	1517883	7885178
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	37815302	16203032
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	438606	229718
Paired Opt. Dupes	3960	1893
% Dupes/100	0.0116	0.0142

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	37784246	16200015
Distinct Read Pairs	37346166	15970340
One Read Pair	36912126	15743449
Two Read Pairs	430032	224151
NRF = Distinct/Total	0.9884	0.9858
PBC1 = OnePair/Distinct	0.9884	0.9858
PBC2 = OnePair/TwoPair	85.8358	70.2359

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	74753392	31946628
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	74753392	31946628
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	74753392	31946628
Paired(QC-failed)	0	0
Read1	37376696	15973314
Read1(QC-failed)	0	0
Read2	37376696	15973314
Read2(QC-failed)	0	0
Properly Paired	74753392	31946628
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	74753392	31946628
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	89336
Np	0
N optimal	89336
N conservative	89336
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.	230
Corr. Est. Fragment Len.	0.1793
Phantom Peak	50
Corr. Phantom Peak	0.1870
Argmin. Corr.	1500
Min. Corr.	0.1729
NSC	1.0367
RSC	0.4519

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	0.0994

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	0.2486
AUC	0.4953
CHANCE divergence	0.1199
Elbow Point	0.0000
JS Distance	0.6285
Synthetic AUC	0.4962
Synthetic Elbow Point	0.1512
Synthetic JS Distance	0.3237