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Report generated at 2020-05-13 22:01:24

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	50196174	153902130
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	45389622	147991110
Mapped(QC-failed)	0	0
% Mapped	90.4200	96.1600
Paired	50196174	153902130
Paired(QC-failed)	0	0
Read1	25098087	76951065
Read1(QC-failed)	0	0
Read2	25098087	76951065
Read2(QC-failed)	0	0
Properly Paired	43567640	138621783
Properly Paired(QC-failed)	0	0
% Properly Paired	86.7900	90.0700
With itself	44216703	144978594
With itself(QC-failed)	0	0
Singletons	1172919	3012516
Singletons(QC-failed)	0	0
% Singleton	2.3400	1.9600
Diff. Chroms	473114	4251163
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	19789043	58423843
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	451342	818600
Paired Opt. Dupes	1451	6310
% Dupes/100	0.0228	0.0140

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	19788879	58422690
Distinct Read Pairs	19337542	57604109
One Read Pair	18895449	56795332
Two Read Pairs	433012	799080
NRF = Distinct/Total	0.9772	0.9860
PBC1 = OnePair/Distinct	0.9771	0.9860
PBC2 = OnePair/TwoPair	43.6372	71.0759

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	38675402	115210486
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	38675402	115210486
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	38675402	115210486
Paired(QC-failed)	0	0
Read1	19337701	57605243
Read1(QC-failed)	0	0
Read2	19337701	57605243
Read2(QC-failed)	0	0
Properly Paired	38675402	115210486
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	38675402	115210486
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	27490
Np	0
N optimal	27490
N conservative	27490
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.	245
Corr. Est. Fragment Len.	0.4923
Phantom Peak	55
Corr. Phantom Peak	0.3964
Argmin. Corr.	1500
Min. Corr.	0.1706
NSC	2.8854
RSC	1.4247

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	0.6284

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	0.0609
AUC	0.4933
CHANCE divergence	0.4766
Elbow Point	0.0000
JS Distance	0.8568
Synthetic AUC	0.4993
Synthetic Elbow Point	0.5243
Synthetic JS Distance	0.6383