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Report generated at 2020-05-14 05:41:00

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	102963120	153902130
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	99442076	147991110
Mapped(QC-failed)	0	0
% Mapped	96.5800	96.1600
Paired	102963120	153902130
Paired(QC-failed)	0	0
Read1	51481560	76951065
Read1(QC-failed)	0	0
Read2	51481560	76951065
Read2(QC-failed)	0	0
Properly Paired	96178405	138621783
Properly Paired(QC-failed)	0	0
% Properly Paired	93.4100	90.0700
With itself	98088629	144978594
With itself(QC-failed)	0	0
Singletons	1353447	3012516
Singletons(QC-failed)	0	0
% Singleton	1.3100	1.9600
Diff. Chroms	1377283	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	42864847	58423843
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	454025	818600
Paired Opt. Dupes	5972	6310
% Dupes/100	0.0106	0.0140

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42864731	58422690
Distinct Read Pairs	42410708	57604109
One Read Pair	41960750	56795332
Two Read Pairs	445927	799080
NRF = Distinct/Total	0.9894	0.9860
PBC1 = OnePair/Distinct	0.9894	0.9860
PBC2 = OnePair/TwoPair	94.0978	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	84821644	115210486
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84821644	115210486
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	84821644	115210486
Paired(QC-failed)	0	0
Read1	42410822	57605243
Read1(QC-failed)	0	0
Read2	42410822	57605243
Read2(QC-failed)	0	0
Properly Paired	84821644	115210486
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	84821644	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	182453
Np	0
N optimal	182453
N conservative	182453
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.	255
Corr. Est. Fragment Len.	0.2127
Phantom Peak	50
Corr. Phantom Peak	0.2000
Argmin. Corr.	1500
Min. Corr.	0.1903
NSC	1.1175
RSC	2.3068

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	0.4374

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	0.1247
AUC	0.4956
CHANCE divergence	0.3505
Elbow Point	0.0000
JS Distance	0.7227
Synthetic AUC	0.5015
Synthetic Elbow Point	0.1849
Synthetic JS Distance	0.4724