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Report generated at 2020-05-13 21:21:34

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	36998524	42861406
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	35936265	41140907
Mapped(QC-failed)	0	0
% Mapped	97.1300	95.9900
Paired	36998524	42861406
Paired(QC-failed)	0	0
Read1	18499262	21430703
Read1(QC-failed)	0	0
Read2	18499262	21430703
Read2(QC-failed)	0	0
Properly Paired	34982626	38139893
Properly Paired(QC-failed)	0	0
% Properly Paired	94.5500	88.9800
With itself	35385691	39997010
With itself(QC-failed)	0	0
Singletons	550574	1143897
Singletons(QC-failed)	0	0
% Singleton	1.4900	2.6700
Diff. Chroms	306448	1200583
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	15694159	15792602
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	164588	138108
Paired Opt. Dupes	2370	676
% Dupes/100	0.0105	0.0087

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	15693165	15791243
Distinct Read Pairs	15528585	15653151
One Read Pair	15365423	15516083
Two Read Pairs	161755	136050
NRF = Distinct/Total	0.9895	0.9913
PBC1 = OnePair/Distinct	0.9895	0.9912
PBC2 = OnePair/TwoPair	94.9920	114.0469

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	31059142	31308988
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	31059142	31308988
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	31059142	31308988
Paired(QC-failed)	0	0
Read1	15529571	15654494
Read1(QC-failed)	0	0
Read2	15529571	15654494
Read2(QC-failed)	0	0
Properly Paired	31059142	31308988
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	31059142	31308988
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	61231
Np	0
N optimal	61231
N conservative	61231
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.	260
Corr. Est. Fragment Len.	0.2113
Phantom Peak	55
Corr. Phantom Peak	0.1997
Argmin. Corr.	1500
Min. Corr.	0.1860
NSC	1.1363
RSC	1.8467

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	0.2076

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	0.1249
AUC	0.4926
CHANCE divergence	0.4568
Elbow Point	0.0000
JS Distance	0.7006
Synthetic AUC	0.5015
Synthetic Elbow Point	0.1403
Synthetic JS Distance	0.4019