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Report generated at 2021-02-05 13:50:09

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	57054014	126012150
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	54908739	124283922
Mapped(QC-failed)	0	0
% Mapped	96.2400	98.6300
Paired	57054014	126012150
Paired(QC-failed)	0	0
Read1	28527007	63006075
Read1(QC-failed)	0	0
Read2	28527007	63006075
Read2(QC-failed)	0	0
Properly Paired	54356799	120756755
Properly Paired(QC-failed)	0	0
% Properly Paired	95.2700	95.8300
With itself	54646691	123573365
With itself(QC-failed)	0	0
Singletons	262048	710557
Singletons(QC-failed)	0	0
% Singleton	0.4600	0.5600
Diff. Chroms	28098	156752
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	25128322	52700713
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2058273	316838
Paired Opt. Dupes	15223	77810
% Dupes/100	0.0819	0.0060

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	25125674	52686084
Distinct Read Pairs	23067611	52369782
One Read Pair	21197251	52065772
Two Read Pairs	1719976	298643
NRF = Distinct/Total	0.9181	0.9940
PBC1 = OnePair/Distinct	0.9189	0.9942
PBC2 = OnePair/TwoPair	12.3242	174.3412

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	46140098	104767750
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	46140098	104767750
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	46140098	104767750
Paired(QC-failed)	0	0
Read1	23070049	52383875
Read1(QC-failed)	0	0
Read2	23070049	52383875
Read2(QC-failed)	0	0
Properly Paired	46140098	104767750
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	46140098	104767750
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	113991
Np	0
N optimal	113991
N conservative	113991
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.	145
Corr. Est. Fragment Len.	0.2426
Phantom Peak	55
Corr. Phantom Peak	0.1873
Argmin. Corr.	1500
Min. Corr.	0.1531
NSC	1.5848
RSC	2.6170

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	0.4072

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	0.1690
AUC	0.4938
CHANCE divergence	0.1728
Elbow Point	0.0000
JS Distance	0.7747
Synthetic AUC	0.5010
Synthetic Elbow Point	0.3627
Synthetic JS Distance	0.4638