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Report generated at 2020-06-06 04:09:20

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	97251240	112182380
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	91929700	109790253
Mapped(QC-failed)	0	0
% Mapped	94.5300	97.8700
Paired	97251240	112182380
Paired(QC-failed)	0	0
Read1	48625620	56091190
Read1(QC-failed)	0	0
Read2	48625620	56091190
Read2(QC-failed)	0	0
Properly Paired	90619164	108525002
Properly Paired(QC-failed)	0	0
% Properly Paired	93.1800	96.7400
With itself	91161203	109236439
With itself(QC-failed)	0	0
Singletons	768497	553814
Singletons(QC-failed)	0	0
% Singleton	0.7900	0.4900
Diff. Chroms	147853	375652
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	38316336	47985328
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6415294	3406443
Paired Opt. Dupes	6018	6385
% Dupes/100	0.1674	0.0710

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	38315432	47950662
Distinct Read Pairs	31900272	44546906
One Read Pair	26560351	41387200
Two Read Pairs	4442208	2936901
NRF = Distinct/Total	0.8326	0.9290
PBC1 = OnePair/Distinct	0.8326	0.9291
PBC2 = OnePair/TwoPair	5.9791	14.0921

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	63802084	89157770
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	63802084	89157770
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	63802084	89157770
Paired(QC-failed)	0	0
Read1	31901042	44578885
Read1(QC-failed)	0	0
Read2	31901042	44578885
Read2(QC-failed)	0	0
Properly Paired	63802084	89157770
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	63802084	89157770
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	23020
Np	0
N optimal	23020
N conservative	23020
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.	205
Corr. Est. Fragment Len.	0.1741
Phantom Peak	50
Corr. Phantom Peak	0.1976
Argmin. Corr.	1500
Min. Corr.	0.1687
NSC	1.0321
RSC	0.1872

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	0.0174

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	0.3002
AUC	0.4949
CHANCE divergence	0.1084
Elbow Point	0.0000
JS Distance	0.5389
Synthetic AUC	0.4958
Synthetic Elbow Point	0.0505
Synthetic JS Distance	0.2424