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Report generated at 2020-05-02 14:24:11

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	37617188	61218190
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	33208127	56551423
Mapped(QC-failed)	0	0
% Mapped	88.2800	92.3800
Paired	37617188	61218190
Paired(QC-failed)	0	0
Read1	18808594	30609095
Read1(QC-failed)	0	0
Read2	18808594	30609095
Read2(QC-failed)	0	0
Properly Paired	31814513	43002956
Properly Paired(QC-failed)	0	0
% Properly Paired	84.5700	70.2500
With itself	32496200	54252491
With itself(QC-failed)	0	0
Singletons	711927	2298932
Singletons(QC-failed)	0	0
% Singleton	1.8900	3.7600
Diff. Chroms	491591	7885108
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	14315673	16203268
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	188947	229841
Paired Opt. Dupes	1440	1894
% Dupes/100	0.0132	0.0142

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	14289427	16200244
Distinct Read Pairs	14100977	15970447
One Read Pair	13914611	15743445
Two Read Pairs	184304	224250
NRF = Distinct/Total	0.9868	0.9858
PBC1 = OnePair/Distinct	0.9868	0.9858
PBC2 = OnePair/TwoPair	75.4981	70.2049

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	28253452	31946854
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	28253452	31946854
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	28253452	31946854
Paired(QC-failed)	0	0
Read1	14126726	15973427
Read1(QC-failed)	0	0
Read2	14126726	15973427
Read2(QC-failed)	0	0
Properly Paired	28253452	31946854
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	28253452	31946854
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	59943
Np	0
N optimal	59943
N conservative	59943
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.	240
Corr. Est. Fragment Len.	0.2109
Phantom Peak	50
Corr. Phantom Peak	0.2122
Argmin. Corr.	1500
Min. Corr.	0.1849
NSC	1.1406
RSC	0.9509

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	0.2877

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	0.1618
AUC	0.4923
CHANCE divergence	0.2527
Elbow Point	0.0000
JS Distance	0.7266
Synthetic AUC	0.5039
Synthetic Elbow Point	0.2190
Synthetic JS Distance	0.4315