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Report generated at 2020-07-14 15:25:05

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	53630896	62419198
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	42565702	59332530
Mapped(QC-failed)	0	0
% Mapped	79.3700	95.0500
Paired	53630896	62419198
Paired(QC-failed)	0	0
Read1	26815448	31209599
Read1(QC-failed)	0	0
Read2	26815448	31209599
Read2(QC-failed)	0	0
Properly Paired	38764281	52460965
Properly Paired(QC-failed)	0	0
% Properly Paired	72.2800	84.0500
With itself	40902252	57668794
With itself(QC-failed)	0	0
Singletons	1663450	1663736
Singletons(QC-failed)	0	0
% Singleton	3.1000	2.6700
Diff. Chroms	1418356	3447531
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	15809657	21847315
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	356689	249453
Paired Opt. Dupes	1135	2581
% Dupes/100	0.0226	0.0114

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	15803138	21831616
Distinct Read Pairs	15446613	21582603
One Read Pair	15096862	21335971
Two Read Pairs	343088	244266
NRF = Distinct/Total	0.9774	0.9886
PBC1 = OnePair/Distinct	0.9774	0.9886
PBC2 = OnePair/TwoPair	44.0029	87.3473

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	30905936	43195724
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	30905936	43195724
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	30905936	43195724
Paired(QC-failed)	0	0
Read1	15452968	21597862
Read1(QC-failed)	0	0
Read2	15452968	21597862
Read2(QC-failed)	0	0
Properly Paired	30905936	43195724
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	30905936	43195724
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	39527
Np	0
N optimal	39527
N conservative	39527
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.	225
Corr. Est. Fragment Len.	0.2005
Phantom Peak	50
Corr. Phantom Peak	0.2086
Argmin. Corr.	1500
Min. Corr.	0.1837
NSC	1.0919
RSC	0.6775

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	0.0936

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	0.1821
AUC	0.4926
CHANCE divergence	0.2791
Elbow Point	0.0000
JS Distance	0.6544
Synthetic AUC	0.5082
Synthetic Elbow Point	0.1127
Synthetic JS Distance	0.3647