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Report generated at 2019-11-03 01:24:23

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	63754920	149933526
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	62198609	146624545
Mapped(QC-failed)	0	0
% Mapped	97.5600	97.7900
Paired	63754920	149933526
Paired(QC-failed)	0	0
Read1	31877460	74966763
Read1(QC-failed)	0	0
Read2	31877460	74966763
Read2(QC-failed)	0	0
Properly Paired	61105604	143525972
Properly Paired(QC-failed)	0	0
% Properly Paired	95.8400	95.7300
With itself	61894724	145761822
With itself(QC-failed)	0	0
Singletons	303885	862723
Singletons(QC-failed)	0	0
% Singleton	0.4800	0.5800
Diff. Chroms	161854	564786
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	27700369	63655918
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1582667	1138162
Paired Opt. Dupes	8929	22681
% Dupes/100	0.0571	0.0179

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	27694822	63588650
Distinct Read Pairs	26112437	62452487
One Read Pair	24604449	61334967
Two Read Pairs	1436517	1100229
NRF = Distinct/Total	0.9429	0.9821
PBC1 = OnePair/Distinct	0.9423	0.9821
PBC2 = OnePair/TwoPair	17.1279	55.7475

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	52235404	125035512
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	52235404	125035512
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	52235404	125035512
Paired(QC-failed)	0	0
Read1	26117702	62517756
Read1(QC-failed)	0	0
Read2	26117702	62517756
Read2(QC-failed)	0	0
Properly Paired	52235404	125035512
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	52235404	125035512
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	66111
Np	0
N optimal	66111
N conservative	66111
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.	150
Corr. Est. Fragment Len.	0.1785
Phantom Peak	50
Corr. Phantom Peak	0.1817
Argmin. Corr.	1500
Min. Corr.	0.1669
NSC	1.0698
RSC	0.7841

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	0.1777

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	0.2634
AUC	0.4944
CHANCE divergence	0.1159
Elbow Point	0.0000
JS Distance	0.6308
Synthetic AUC	0.5066
Synthetic Elbow Point	0.2115
Synthetic JS Distance	0.3118