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Report generated at 2021-06-17 08:43:44

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	55559694	70039576
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53686104	69332795
Mapped(QC-failed)	0	0
% Mapped	96.6300	98.9900
Paired	55559694	70039576
Paired(QC-failed)	0	0
Read1	27779847	35019788
Read1(QC-failed)	0	0
Read2	27779847	35019788
Read2(QC-failed)	0	0
Properly Paired	53332776	68610065
Properly Paired(QC-failed)	0	0
% Properly Paired	95.9900	97.9600
With itself	53487302	69045229
With itself(QC-failed)	0	0
Singletons	198802	287566
Singletons(QC-failed)	0	0
% Singleton	0.3600	0.4100
Diff. Chroms	20501	71553
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	24544568	30249787
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1178554	280927
Paired Opt. Dupes	30461	64508
% Dupes/100	0.0480	0.0093

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	24543703	30249419
Distinct Read Pairs	23365161	29968493
One Read Pair	22349694	29693357
Two Read Pairs	911968	270900
NRF = Distinct/Total	0.9520	0.9907
PBC1 = OnePair/Distinct	0.9565	0.9908
PBC2 = OnePair/TwoPair	24.5071	109.6100

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	46732028	59937720
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	46732028	59937720
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	46732028	59937720
Paired(QC-failed)	0	0
Read1	23366014	29968860
Read1(QC-failed)	0	0
Read2	23366014	29968860
Read2(QC-failed)	0	0
Properly Paired	46732028	59937720
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	46732028	59937720
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	115807
Np	0
N optimal	115807
N conservative	115807
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.	150
Corr. Est. Fragment Len.	0.3010
Phantom Peak	55
Corr. Phantom Peak	0.1849
Argmin. Corr.	1500
Min. Corr.	0.1474
NSC	2.0415
RSC	4.1027

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	0.6022

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	0.1036
AUC	0.4938
CHANCE divergence	0.2490
Elbow Point	0.0000
JS Distance	0.8693
Synthetic AUC	0.4977
Synthetic Elbow Point	0.4619
Synthetic JS Distance	0.5792