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Report generated at 2020-05-03 16:17:44

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	132727598	143118944
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	120403193	139990469
Mapped(QC-failed)	0	0
% Mapped	90.7100	97.8100
Paired	132727598	143118944
Paired(QC-failed)	0	0
Read1	66363799	71559472
Read1(QC-failed)	0	0
Read2	66363799	71559472
Read2(QC-failed)	0	0
Properly Paired	118046144	137871740
Properly Paired(QC-failed)	0	0
% Properly Paired	88.9400	96.3300
With itself	119368829	139333057
With itself(QC-failed)	0	0
Singletons	1034364	657412
Singletons(QC-failed)	0	0
% Singleton	0.7800	0.4600
Diff. Chroms	739480	791791
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	51703637	60254568
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	252910	215974
Paired Opt. Dupes	2067	979
% Dupes/100	0.0049	0.0036

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	51699732	60210751
Distinct Read Pairs	51446849	59995391
One Read Pair	51195202	59781016
Two Read Pairs	250417	213430
NRF = Distinct/Total	0.9951	0.9964
PBC1 = OnePair/Distinct	0.9951	0.9964
PBC2 = OnePair/TwoPair	204.4398	280.0966

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	102901454	120077188
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	102901454	120077188
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	102901454	120077188
Paired(QC-failed)	0	0
Read1	51450727	60038594
Read1(QC-failed)	0	0
Read2	51450727	60038594
Read2(QC-failed)	0	0
Properly Paired	102901454	120077188
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	102901454	120077188
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	201665
Np	0
N optimal	201665
N conservative	201665
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.	125
Corr. Est. Fragment Len.	0.1857
Phantom Peak	50
Corr. Phantom Peak	0.2056
Argmin. Corr.	1500
Min. Corr.	0.1771
NSC	1.0484
RSC	0.3011

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	0.2356

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	0.2539
AUC	0.4960
CHANCE divergence	0.1046
Elbow Point	0.0000
JS Distance	0.6529
Synthetic AUC	0.4995
Synthetic Elbow Point	0.1755
Synthetic JS Distance	0.3250