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Report generated at 2020-06-06 04:03:42

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	92134798	141046192
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	83375147	133545822
Mapped(QC-failed)	0	0
% Mapped	90.4900	94.6800
Paired	92134798	141046192
Paired(QC-failed)	0	0
Read1	46067399	70523096
Read1(QC-failed)	0	0
Read2	46067399	70523096
Read2(QC-failed)	0	0
Properly Paired	82180351	131515734
Properly Paired(QC-failed)	0	0
% Properly Paired	89.2000	93.2400
With itself	82853307	132854680
With itself(QC-failed)	0	0
Singletons	521840	691142
Singletons(QC-failed)	0	0
% Singleton	0.5700	0.4900
Diff. Chroms	96920	243760
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	37185561	58232424
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	12986617	4001234
Paired Opt. Dupes	141646	6761
% Dupes/100	0.3492	0.0687

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	37164766	57912757
Distinct Read Pairs	24185640	53959656
One Read Pair	15643295	50262057
Two Read Pairs	5560891	3464802
NRF = Distinct/Total	0.6508	0.9317
PBC1 = OnePair/Distinct	0.6468	0.9315
PBC2 = OnePair/TwoPair	2.8131	14.5065

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	48397888	108462380
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	48397888	108462380
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	48397888	108462380
Paired(QC-failed)	0	0
Read1	24198944	54231190
Read1(QC-failed)	0	0
Read2	24198944	54231190
Read2(QC-failed)	0	0
Properly Paired	48397888	108462380
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	48397888	108462380
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	110851
Np	0
N optimal	110851
N conservative	110851
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.	140
Corr. Est. Fragment Len.	0.1977
Phantom Peak	50
Corr. Phantom Peak	0.1890
Argmin. Corr.	1500
Min. Corr.	0.1570
NSC	1.2590
RSC	1.2717

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	0.3343

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	0.1953
AUC	0.4942
CHANCE divergence	0.1477
Elbow Point	0.0000
JS Distance	0.7336
Synthetic AUC	0.4992
Synthetic Elbow Point	0.3066
Synthetic JS Distance	0.4219