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Report generated at 2020-05-14 04:14:41

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	103441600	42861406
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	99854051	41140907
Mapped(QC-failed)	0	0
% Mapped	96.5300	95.9900
Paired	103441600	42861406
Paired(QC-failed)	0	0
Read1	51720800	21430703
Read1(QC-failed)	0	0
Read2	51720800	21430703
Read2(QC-failed)	0	0
Properly Paired	97103955	38139893
Properly Paired(QC-failed)	0	0
% Properly Paired	93.8700	88.9800
With itself	98220999	39997010
With itself(QC-failed)	0	0
Singletons	1633052	1143897
Singletons(QC-failed)	0	0
% Singleton	1.5800	2.6700
Diff. Chroms	884228	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	44507298	15792602
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1782659	138108
Paired Opt. Dupes	7762	676
% Dupes/100	0.0401	0.0087

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	44502136	15791243
Distinct Read Pairs	42719689	15653151
One Read Pair	40997767	15516083
Two Read Pairs	1663306	136050
NRF = Distinct/Total	0.9599	0.9913
PBC1 = OnePair/Distinct	0.9597	0.9912
PBC2 = OnePair/TwoPair	24.6484	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	85449278	31308988
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	85449278	31308988
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	85449278	31308988
Paired(QC-failed)	0	0
Read1	42724639	15654494
Read1(QC-failed)	0	0
Read2	42724639	15654494
Read2(QC-failed)	0	0
Properly Paired	85449278	31308988
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	85449278	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	33687
Np	0
N optimal	33687
N conservative	33687
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.	265
Corr. Est. Fragment Len.	0.4565
Phantom Peak	55
Corr. Phantom Peak	0.3867
Argmin. Corr.	1500
Min. Corr.	0.2022
NSC	2.2572
RSC	1.3782

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	0.6657

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	0.0626
AUC	0.4955
CHANCE divergence	0.3840
Elbow Point	0.0000
JS Distance	0.9031
Synthetic AUC	0.5045
Synthetic Elbow Point	0.5485
Synthetic JS Distance	0.6674