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Report generated at 2020-05-23 00:52:46

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	130039648	135840732
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	123896971	133934829
Mapped(QC-failed)	0	0
% Mapped	95.2800	98.6000
Paired	130039648	135840732
Paired(QC-failed)	0	0
Read1	65019824	67920366
Read1(QC-failed)	0	0
Read2	65019824	67920366
Read2(QC-failed)	0	0
Properly Paired	121324315	128263399
Properly Paired(QC-failed)	0	0
% Properly Paired	93.3000	94.4200
With itself	122589876	133179397
With itself(QC-failed)	0	0
Singletons	1307095	755432
Singletons(QC-failed)	0	0
% Singleton	1.0100	0.5600
Diff. Chroms	152482	132252
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	49842625	56898377
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	15435640	573921
Paired Opt. Dupes	4851	4663
% Dupes/100	0.3097	0.0101

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49831383	56891592
Distinct Read Pairs	34399028	56317967
One Read Pair	22863127	55773200
Two Read Pairs	8478458	533976
NRF = Distinct/Total	0.6903	0.9899
PBC1 = OnePair/Distinct	0.6646	0.9903
PBC2 = OnePair/TwoPair	2.6966	104.4489

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	68813970	112648912
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	68813970	112648912
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	68813970	112648912
Paired(QC-failed)	0	0
Read1	34406985	56324456
Read1(QC-failed)	0	0
Read2	34406985	56324456
Read2(QC-failed)	0	0
Properly Paired	68813970	112648912
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	68813970	112648912
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	41950
Np	0
N optimal	41950
N conservative	41950
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.	0.1777
Phantom Peak	50
Corr. Phantom Peak	0.1995
Argmin. Corr.	1500
Min. Corr.	0.1669
NSC	1.0649
RSC	0.3323

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	0.0469

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	0.3124
AUC	0.4951
CHANCE divergence	0.0980
Elbow Point	0.0000
JS Distance	0.5428
Synthetic AUC	0.4989
Synthetic Elbow Point	0.0724
Synthetic JS Distance	0.2290