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Report generated at 2020-11-26 00:20:30

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	119397142	175533488
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	117761091	173335756
Mapped(QC-failed)	0	0
% Mapped	98.6300	98.7500
Paired	119397142	175533488
Paired(QC-failed)	0	0
Read1	59698571	87766744
Read1(QC-failed)	0	0
Read2	59698571	87766744
Read2(QC-failed)	0	0
Properly Paired	115252046	163308151
Properly Paired(QC-failed)	0	0
% Properly Paired	96.5300	93.0400
With itself	117151799	171954135
With itself(QC-failed)	0	0
Singletons	609292	1381621
Singletons(QC-failed)	0	0
% Singleton	0.5100	0.7900
Diff. Chroms	1252512	6449411
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	49224070	68251656
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6133547	5232900
Paired Opt. Dupes	8418	11153
% Dupes/100	0.1246	0.0767

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49223814	68241180
Distinct Read Pairs	43090299	63009077
One Read Pair	37600827	58069038
Two Read Pairs	4907185	4666343
NRF = Distinct/Total	0.8754	0.9233
PBC1 = OnePair/Distinct	0.8726	0.9216
PBC2 = OnePair/TwoPair	7.6624	12.4442

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	86181046	126037512
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	86181046	126037512
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	86181046	126037512
Paired(QC-failed)	0	0
Read1	43090523	63018756
Read1(QC-failed)	0	0
Read2	43090523	63018756
Read2(QC-failed)	0	0
Properly Paired	86181046	126037512
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	86181046	126037512
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	135120
Np	0
N optimal	135120
N conservative	135120
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.	145
Corr. Est. Fragment Len.	0.2243
Phantom Peak	50
Corr. Phantom Peak	0.2242
Argmin. Corr.	1500
Min. Corr.	0.2145
NSC	1.0458
RSC	1.0066

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	0.7737

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	0.0683
AUC	0.4946
CHANCE divergence	0.4001
Elbow Point	0.0000
JS Distance	0.8456
Synthetic AUC	0.4956
Synthetic Elbow Point	0.5254
Synthetic JS Distance	0.6163