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Report generated at 2020-05-30 20:21:08

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	91400730	196505800
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	90721731	193483775
Mapped(QC-failed)	0	0
% Mapped	99.2600	98.4600
Paired	91400730	196505800
Paired(QC-failed)	0	0
Read1	45700365	98252900
Read1(QC-failed)	0	0
Read2	45700365	98252900
Read2(QC-failed)	0	0
Properly Paired	90363210	182597399
Properly Paired(QC-failed)	0	0
% Properly Paired	98.8600	92.9200
With itself	90419644	192397679
With itself(QC-failed)	0	0
Singletons	302087	1086096
Singletons(QC-failed)	0	0
% Singleton	0.3300	0.5500
Diff. Chroms	14031	243413
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	42745137	81193783
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2750360	858603
Paired Opt. Dupes	2913	4308
% Dupes/100	0.0643	0.0106

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42744352	81187332
Distinct Read Pairs	39994023	80329098
One Read Pair	37520618	79518226
Two Read Pairs	2278612	792113
NRF = Distinct/Total	0.9357	0.9894
PBC1 = OnePair/Distinct	0.9382	0.9899
PBC2 = OnePair/TwoPair	16.4664	100.3875

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	79989554	160670360
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	79989554	160670360
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	79989554	160670360
Paired(QC-failed)	0	0
Read1	39994777	80335180
Read1(QC-failed)	0	0
Read2	39994777	80335180
Read2(QC-failed)	0	0
Properly Paired	79989554	160670360
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	79989554	160670360
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	134733
Np	0
N optimal	134733
N conservative	134733
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.	0.2375
Phantom Peak	55
Corr. Phantom Peak	0.1987
Argmin. Corr.	1500
Min. Corr.	0.1792
NSC	1.3255
RSC	2.9920

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	0.6036

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	0.1157
AUC	0.4955
CHANCE divergence	0.1878
Elbow Point	0.0000
JS Distance	0.8272
Synthetic AUC	0.5053
Synthetic Elbow Point	0.4629
Synthetic JS Distance	0.5617