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Report generated at 2020-07-15 18:00:41

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	179258518	143118944
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	167648363	139990469
Mapped(QC-failed)	0	0
% Mapped	93.5200	97.8100
Paired	179258518	143118944
Paired(QC-failed)	0	0
Read1	89629259	71559472
Read1(QC-failed)	0	0
Read2	89629259	71559472
Read2(QC-failed)	0	0
Properly Paired	164612794	137871752
Properly Paired(QC-failed)	0	0
% Properly Paired	91.8300	96.3300
With itself	166437031	139333057
With itself(QC-failed)	0	0
Singletons	1211332	657412
Singletons(QC-failed)	0	0
% Singleton	0.6800	0.4600
Diff. Chroms	1127367	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	74043215	60254678
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	387439	215954
Paired Opt. Dupes	2054	979
% Dupes/100	0.0052	0.0036

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	74039149	60210805
Distinct Read Pairs	73651737	59995465
One Read Pair	73266287	59781108
Two Read Pairs	383504	213413
NRF = Distinct/Total	0.9948	0.9964
PBC1 = OnePair/Distinct	0.9948	0.9964
PBC2 = OnePair/TwoPair	191.0444	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	147311552	120077448
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	147311552	120077448
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	147311552	120077448
Paired(QC-failed)	0	0
Read1	73655776	60038724
Read1(QC-failed)	0	0
Read2	73655776	60038724
Read2(QC-failed)	0	0
Properly Paired	147311552	120077448
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	147311552	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	232902
Np	0
N optimal	232902
N conservative	232902
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.	140
Corr. Est. Fragment Len.	0.1828
Phantom Peak	50
Corr. Phantom Peak	0.1957
Argmin. Corr.	1500
Min. Corr.	0.1747
NSC	1.0460
RSC	0.3845

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	0.2303

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	0.2605
AUC	0.4966
CHANCE divergence	0.1009
Elbow Point	0.0000
JS Distance	0.6487
Synthetic AUC	0.5024
Synthetic Elbow Point	0.1623
Synthetic JS Distance	0.3153