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Report generated at 2020-05-13 07:11:29

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	57288604	55554290
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	54518883	53234328
Mapped(QC-failed)	0	0
% Mapped	95.1700	95.8200
Paired	57288604	55554290
Paired(QC-failed)	0	0
Read1	28644302	27777145
Read1(QC-failed)	0	0
Read2	28644302	27777145
Read2(QC-failed)	0	0
Properly Paired	51646375	46813080
Properly Paired(QC-failed)	0	0
% Properly Paired	90.1500	84.2700
With itself	53561509	52018273
With itself(QC-failed)	0	0
Singletons	957374	1216055
Singletons(QC-failed)	0	0
% Singleton	1.6700	2.1900
Diff. Chroms	1378510	3541644
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	22933081	19892586
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	190032	222592
Paired Opt. Dupes	2952	2281
% Dupes/100	0.0083	0.0112

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	22932901	19890387
Distinct Read Pairs	22742870	19667823
One Read Pair	22554228	19447434
Two Read Pairs	187262	218233
NRF = Distinct/Total	0.9917	0.9888
PBC1 = OnePair/Distinct	0.9917	0.9888
PBC2 = OnePair/TwoPair	120.4421	89.1132

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	45486098	39339988
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	45486098	39339988
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	45486098	39339988
Paired(QC-failed)	0	0
Read1	22743049	19669994
Read1(QC-failed)	0	0
Read2	22743049	19669994
Read2(QC-failed)	0	0
Properly Paired	45486098	39339988
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	45486098	39339988
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	116719
Np	0
N optimal	116719
N conservative	116719
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.	280
Corr. Est. Fragment Len.	0.2134
Phantom Peak	50
Corr. Phantom Peak	0.2054
Argmin. Corr.	1500
Min. Corr.	0.1946
NSC	1.0965
RSC	1.7460

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	0.3806

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	0.1204
AUC	0.4939
CHANCE divergence	0.3947
Elbow Point	0.0000
JS Distance	0.7327
Synthetic AUC	0.4978
Synthetic Elbow Point	0.2059
Synthetic JS Distance	0.4544