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Report generated at 2019-10-12 15:05:44

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	52803894	82773480
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	48092179	80507886
Mapped(QC-failed)	0	0
% Mapped	91.0800	97.2600
Paired	52803894	82773480
Paired(QC-failed)	0	0
Read1	26401947	41386740
Read1(QC-failed)	0	0
Read2	26401947	41386740
Read2(QC-failed)	0	0
Properly Paired	47682009	79812046
Properly Paired(QC-failed)	0	0
% Properly Paired	90.3000	96.4200
With itself	47835038	80154101
With itself(QC-failed)	0	0
Singletons	257141	353785
Singletons(QC-failed)	0	0
% Singleton	0.4900	0.4300
Diff. Chroms	48329	116542
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	21598905	35609282
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	16390044	3238943
Paired Opt. Dupes	5730	8059
% Dupes/100	0.7588	0.0910

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	21598034	35576205
Distinct Read Pairs	5208600	32340103
One Read Pair	1347954	29415039
Two Read Pairs	911250	2647904
NRF = Distinct/Total	0.2412	0.9090
PBC1 = OnePair/Distinct	0.2588	0.9096
PBC2 = OnePair/TwoPair	1.4792	11.1088

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	10417722	64740678
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	10417722	64740678
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	10417722	64740678
Paired(QC-failed)	0	0
Read1	5208861	32370339
Read1(QC-failed)	0	0
Read2	5208861	32370339
Read2(QC-failed)	0	0
Properly Paired	10417722	64740678
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	10417722	64740678
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	84722
Np	0
N optimal	84722
N conservative	84722
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.	170
Corr. Est. Fragment Len.	0.0587
Phantom Peak	50
Corr. Phantom Peak	0.0579
Argmin. Corr.	1500
Min. Corr.	0.0518
NSC	1.1343
RSC	1.1362

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	0.1574

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	0.1417
AUC	0.4874
CHANCE divergence	0.4913
Elbow Point	0.0000
JS Distance	0.6214
Synthetic AUC	0.5209
Synthetic Elbow Point	0.1323
Synthetic JS Distance	0.3114