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Report generated at 2020-07-01 23:31:07

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	286275790	175026970
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	280149036	171819449
Mapped(QC-failed)	0	0
% Mapped	97.8600	98.1700
Paired	286275790	175026970
Paired(QC-failed)	0	0
Read1	143137895	87513485
Read1(QC-failed)	0	0
Read2	143137895	87513485
Read2(QC-failed)	0	0
Properly Paired	273704077	168294504
Properly Paired(QC-failed)	0	0
% Properly Paired	95.6100	96.1500
With itself	277303914	170965030
With itself(QC-failed)	0	0
Singletons	2845122	854419
Singletons(QC-failed)	0	0
% Singleton	0.9900	0.4900
Diff. Chroms	366190	1256637
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	124220340	74969886
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	10209763	1349559
Paired Opt. Dupes	4697	20206
% Dupes/100	0.0822	0.0180

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	124210375	74828450
Distinct Read Pairs	114001814	73485191
One Read Pair	104642554	72156446
Two Read Pairs	8582597	1315888
NRF = Distinct/Total	0.9178	0.9820
PBC1 = OnePair/Distinct	0.9179	0.9819
PBC2 = OnePair/TwoPair	12.1924	54.8348

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	228021154	147240654
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	228021154	147240654
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	228021154	147240654
Paired(QC-failed)	0	0
Read1	114010577	73620327
Read1(QC-failed)	0	0
Read2	114010577	73620327
Read2(QC-failed)	0	0
Properly Paired	228021154	147240654
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	228021154	147240654
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	209769
Np	0
N optimal	209769
N conservative	209769
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.	210
Corr. Est. Fragment Len.	0.1893
Phantom Peak	50
Corr. Phantom Peak	0.1930
Argmin. Corr.	1500
Min. Corr.	0.1794
NSC	1.0550
RSC	0.7238

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	0.5508

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	0.1841
AUC	0.4973
CHANCE divergence	0.0944
Elbow Point	0.0000
JS Distance	0.7853
Synthetic AUC	0.5034
Synthetic Elbow Point	0.3558
Synthetic JS Distance	0.4558