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Report generated at 2020-06-08 17:20:15

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	356151640	115682520
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	339503926	110134971
Mapped(QC-failed)	0	0
% Mapped	95.3300	95.2000
Paired	356151640	115682520
Paired(QC-failed)	0	0
Read1	178075820	57841260
Read1(QC-failed)	0	0
Read2	178075820	57841260
Read2(QC-failed)	0	0
Properly Paired	325134637	104877572
Properly Paired(QC-failed)	0	0
% Properly Paired	91.2900	90.6600
With itself	327074782	106096680
With itself(QC-failed)	0	0
Singletons	12429144	4038291
Singletons(QC-failed)	0	0
% Singleton	3.4900	3.4900
Diff. Chroms	981054	752703
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	133332437	44142992
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	19526401	1315627
Paired Opt. Dupes	12002	4864
% Dupes/100	0.1464	0.0298

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	133329250	44112531
Distinct Read Pairs	113803315	42798076
One Read Pair	97092177	41528009
Two Read Pairs	14307275	1233402
NRF = Distinct/Total	0.8536	0.9702
PBC1 = OnePair/Distinct	0.8532	0.9703
PBC2 = OnePair/TwoPair	6.7862	33.6695

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	227612072	85654730
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	227612072	85654730
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	227612072	85654730
Paired(QC-failed)	0	0
Read1	113806036	42827365
Read1(QC-failed)	0	0
Read2	113806036	42827365
Read2(QC-failed)	0	0
Properly Paired	227612072	85654730
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	227612072	85654730
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	98422
Np	0
N optimal	98422
N conservative	98422
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.	120
Corr. Est. Fragment Len.	0.1765
Phantom Peak	50
Corr. Phantom Peak	0.1890
Argmin. Corr.	1500
Min. Corr.	0.1712
NSC	1.0311
RSC	0.2979

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	0.0797

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	0.3285
AUC	0.4973
CHANCE divergence	0.0953
Elbow Point	0.0000
JS Distance	0.5473
Synthetic AUC	0.5019
Synthetic Elbow Point	0.0718
Synthetic JS Distance	0.2148