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Report generated at 2019-11-01 02:52:55

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	126423158	345403306
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	124606163	341696882
Mapped(QC-failed)	0	0
% Mapped	98.5600	98.9300
Paired	126423158	345403306
Paired(QC-failed)	0	0
Read1	63211579	172701653
Read1(QC-failed)	0	0
Read2	63211579	172701653
Read2(QC-failed)	0	0
Properly Paired	122264312	332198812
Properly Paired(QC-failed)	0	0
% Properly Paired	96.7100	96.1800
With itself	123757308	339827021
With itself(QC-failed)	0	0
Singletons	848855	1869861
Singletons(QC-failed)	0	0
% Singleton	0.6700	0.5400
Diff. Chroms	1100001	4989385
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	54727656	139165923
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	5018350	13769945
Paired Opt. Dupes	9917	20499
% Dupes/100	0.0917	0.0989

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	54725230	139068773
Distinct Read Pairs	49707063	125309978
One Read Pair	45080877	112707049
Two Read Pairs	4261781	11538367
NRF = Distinct/Total	0.9083	0.9011
PBC1 = OnePair/Distinct	0.9069	0.8994
PBC2 = OnePair/TwoPair	10.5779	9.7680

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	99418612	250791956
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	99418612	250791956
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	99418612	250791956
Paired(QC-failed)	0	0
Read1	49709306	125395978
Read1(QC-failed)	0	0
Read2	49709306	125395978
Read2(QC-failed)	0	0
Properly Paired	99418612	250791956
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	99418612	250791956
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	35136
Np	0
N optimal	35136
N conservative	35136
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.	0.4471
Phantom Peak	55
Corr. Phantom Peak	0.4097
Argmin. Corr.	1500
Min. Corr.	0.1907
NSC	2.3450
RSC	1.1707

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	0.6420

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	0.1115
AUC	0.4950
CHANCE divergence	0.1288
Elbow Point	0.0000
JS Distance	0.9557
Synthetic AUC	0.5059
Synthetic Elbow Point	0.6018
Synthetic JS Distance	0.6392