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Report generated at 2019-11-01 14:33:04

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	221395054	345403306
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	218850438	341696882
Mapped(QC-failed)	0	0
% Mapped	98.8500	98.9300
Paired	221395054	345403306
Paired(QC-failed)	0	0
Read1	110697527	172701653
Read1(QC-failed)	0	0
Read2	110697527	172701653
Read2(QC-failed)	0	0
Properly Paired	215268934	332198812
Properly Paired(QC-failed)	0	0
% Properly Paired	97.2300	96.1800
With itself	217646145	339827021
With itself(QC-failed)	0	0
Singletons	1204293	1869861
Singletons(QC-failed)	0	0
% Singleton	0.5400	0.5400
Diff. Chroms	1618670	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	93883818	139165923
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	10727397	13769945
Paired Opt. Dupes	22062	20499
% Dupes/100	0.1143	0.0989

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	93879177	139068773
Distinct Read Pairs	83152262	125309978
One Read Pair	73455499	112707049
Two Read Pairs	8754133	11538367
NRF = Distinct/Total	0.8857	0.9011
PBC1 = OnePair/Distinct	0.8834	0.8994
PBC2 = OnePair/TwoPair	8.3910	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	166312842	250791956
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	166312842	250791956
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	166312842	250791956
Paired(QC-failed)	0	0
Read1	83156421	125395978
Read1(QC-failed)	0	0
Read2	83156421	125395978
Read2(QC-failed)	0	0
Properly Paired	166312842	250791956
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	166312842	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	135137
Np	0
N optimal	135137
N conservative	135137
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.	215
Corr. Est. Fragment Len.	0.1899
Phantom Peak	50
Corr. Phantom Peak	0.1906
Argmin. Corr.	1500
Min. Corr.	0.1778
NSC	1.0685
RSC	0.9494

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	0.4818

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	0.2045
AUC	0.4961
CHANCE divergence	0.1084
Elbow Point	0.0000
JS Distance	0.8206
Synthetic AUC	0.5058
Synthetic Elbow Point	0.3442
Synthetic JS Distance	0.4229