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Report generated at 2020-07-22 21:31:07

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	158945062	100538574
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	156688068	98863286
Mapped(QC-failed)	0	0
% Mapped	98.5800	98.3300
Paired	158945062	100538574
Paired(QC-failed)	0	0
Read1	79472531	50269287
Read1(QC-failed)	0	0
Read2	79472531	50269287
Read2(QC-failed)	0	0
Properly Paired	155408102	94514238
Properly Paired(QC-failed)	0	0
% Properly Paired	97.7700	94.0100
With itself	155792604	98221443
With itself(QC-failed)	0	0
Singletons	895464	641843
Singletons(QC-failed)	0	0
% Singleton	0.5600	0.6400
Diff. Chroms	62364	127393
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	68071884	42061680
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2349236	280885
Paired Opt. Dupes	2585	1456
% Dupes/100	0.0345	0.0067

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	68068581	42052025
Distinct Read Pairs	65719468	41772167
One Read Pair	63442470	41504154
Two Read Pairs	2207959	263367
NRF = Distinct/Total	0.9655	0.9933
PBC1 = OnePair/Distinct	0.9654	0.9936
PBC2 = OnePair/TwoPair	28.7335	157.5906

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	131445296	83561590
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	131445296	83561590
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	131445296	83561590
Paired(QC-failed)	0	0
Read1	65722648	41780795
Read1(QC-failed)	0	0
Read2	65722648	41780795
Read2(QC-failed)	0	0
Properly Paired	131445296	83561590
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	131445296	83561590
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	127795
Np	0
N optimal	127795
N conservative	127795
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.	-5
Corr. Est. Fragment Len.	0.1783
Phantom Peak	50
Corr. Phantom Peak	0.1822
Argmin. Corr.	1500
Min. Corr.	0.1714
NSC	1.0401
RSC	0.6394

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	0.1179

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	0.2833
AUC	0.4965
CHANCE divergence	0.1004
Elbow Point	0.0000
JS Distance	0.5630
Synthetic AUC	0.5049
Synthetic Elbow Point	0.0817
Synthetic JS Distance	0.2790