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Report generated at 2020-05-22 20:19:41

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	37324164	122032658
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	35415174	118962872
Mapped(QC-failed)	0	0
% Mapped	94.8900	97.4800
Paired	37324164	122032658
Paired(QC-failed)	0	0
Read1	18662082	61016329
Read1(QC-failed)	0	0
Read2	18662082	61016329
Read2(QC-failed)	0	0
Properly Paired	34680146	114858760
Properly Paired(QC-failed)	0	0
% Properly Paired	92.9200	94.1200
With itself	34932842	117388354
With itself(QC-failed)	0	0
Singletons	482332	1574518
Singletons(QC-failed)	0	0
% Singleton	1.2900	1.2900
Diff. Chroms	156316	1710423
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	15713487	49902005
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	253766	628189
Paired Opt. Dupes	3411	7684
% Dupes/100	0.0162	0.0126

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	15713000	49898886
Distinct Read Pairs	15459238	49270740
One Read Pair	15208889	48649123
Two Read Pairs	246980	615143
NRF = Distinct/Total	0.9839	0.9874
PBC1 = OnePair/Distinct	0.9838	0.9874
PBC2 = OnePair/TwoPair	61.5794	79.0859

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	30919442	98547632
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	30919442	98547632
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	30919442	98547632
Paired(QC-failed)	0	0
Read1	15459721	49273816
Read1(QC-failed)	0	0
Read2	15459721	49273816
Read2(QC-failed)	0	0
Properly Paired	30919442	98547632
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	30919442	98547632
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	94662
Np	0
N optimal	94662
N conservative	94662
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.	275
Corr. Est. Fragment Len.	0.2335
Phantom Peak	50
Corr. Phantom Peak	0.2178
Argmin. Corr.	1500
Min. Corr.	0.1994
NSC	1.1710
RSC	1.8582

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	0.4270

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	0.0969
AUC	0.4926
CHANCE divergence	0.4827
Elbow Point	0.0000
JS Distance	0.7550
Synthetic AUC	0.5063
Synthetic Elbow Point	0.2460
Synthetic JS Distance	0.4723