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Report generated at 2020-05-22 18:01:47

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	79435720	122032658
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	76698063	118962872
Mapped(QC-failed)	0	0
% Mapped	96.5500	97.4800
Paired	79435720	122032658
Paired(QC-failed)	0	0
Read1	39717860	61016329
Read1(QC-failed)	0	0
Read2	39717860	61016329
Read2(QC-failed)	0	0
Properly Paired	75056748	114858760
Properly Paired(QC-failed)	0	0
% Properly Paired	94.4900	94.1200
With itself	75722150	117388354
With itself(QC-failed)	0	0
Singletons	975913	1574518
Singletons(QC-failed)	0	0
% Singleton	1.2300	1.2900
Diff. Chroms	430942	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	33663605	49902005
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	315588	628189
Paired Opt. Dupes	3648	7684
% Dupes/100	0.0094	0.0126

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	33661339	49898886
Distinct Read Pairs	33345771	49270740
One Read Pair	33032705	48649123
Two Read Pairs	310584	615143
NRF = Distinct/Total	0.9906	0.9874
PBC1 = OnePair/Distinct	0.9906	0.9874
PBC2 = OnePair/TwoPair	106.3568	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	66696034	98547632
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	66696034	98547632
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	66696034	98547632
Paired(QC-failed)	0	0
Read1	33348017	49273816
Read1(QC-failed)	0	0
Read2	33348017	49273816
Read2(QC-failed)	0	0
Properly Paired	66696034	98547632
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	66696034	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	135031
Np	0
N optimal	135031
N conservative	135031
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.	0.1964
Phantom Peak	50
Corr. Phantom Peak	0.1905
Argmin. Corr.	1500
Min. Corr.	0.1827
NSC	1.0750
RSC	1.7630

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	0.2003

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	0.1481
AUC	0.4950
CHANCE divergence	0.3470
Elbow Point	0.0000
JS Distance	0.6943
Synthetic AUC	0.4963
Synthetic Elbow Point	0.0980
Synthetic JS Distance	0.4138