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Report generated at 2020-07-14 18:59:59

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	49286550	143118944
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	46953210	139990469
Mapped(QC-failed)	0	0
% Mapped	95.2700	97.8100
Paired	49286550	143118944
Paired(QC-failed)	0	0
Read1	24643275	71559472
Read1(QC-failed)	0	0
Read2	24643275	71559472
Read2(QC-failed)	0	0
Properly Paired	46218532	137871752
Properly Paired(QC-failed)	0	0
% Properly Paired	93.7800	96.3300
With itself	46690253	139333057
With itself(QC-failed)	0	0
Singletons	262957	657412
Singletons(QC-failed)	0	0
% Singleton	0.5300	0.4600
Diff. Chroms	290855	791653
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	20836850	60254678
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	58989	215954
Paired Opt. Dupes	485	979
% Dupes/100	0.0028	0.0036

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	20835507	60210805
Distinct Read Pairs	20776520	59995465
One Read Pair	20717646	59781108
Two Read Pairs	58761	213413
NRF = Distinct/Total	0.9972	0.9964
PBC1 = OnePair/Distinct	0.9972	0.9964
PBC2 = OnePair/TwoPair	352.5748	280.1193

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	41555722	120077448
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	41555722	120077448
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	41555722	120077448
Paired(QC-failed)	0	0
Read1	20777861	60038724
Read1(QC-failed)	0	0
Read2	20777861	60038724
Read2(QC-failed)	0	0
Properly Paired	41555722	120077448
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	41555722	120077448
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	100097
Np	0
N optimal	100097
N conservative	100097
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.	0.1847
Phantom Peak	50
Corr. Phantom Peak	0.1956
Argmin. Corr.	1500
Min. Corr.	0.1753
NSC	1.0536
RSC	0.4646

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	0.1639

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	0.2340
AUC	0.4937
CHANCE divergence	0.1481
Elbow Point	0.0000
JS Distance	0.6368
Synthetic AUC	0.5114
Synthetic Elbow Point	0.1913
Synthetic JS Distance	0.3341