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Report generated at 2019-11-01 11:24:50

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	124339940	317909612
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	122674726	312072580
Mapped(QC-failed)	0	0
% Mapped	98.6600	98.1600
Paired	124339940	317909612
Paired(QC-failed)	0	0
Read1	62169970	158954806
Read1(QC-failed)	0	0
Read2	62169970	158954806
Read2(QC-failed)	0	0
Properly Paired	120029351	294728580
Properly Paired(QC-failed)	0	0
% Properly Paired	96.5300	92.7100
With itself	122113443	309884253
With itself(QC-failed)	0	0
Singletons	561283	2188327
Singletons(QC-failed)	0	0
% Singleton	0.4500	0.6900
Diff. Chroms	1019236	9012143
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	51091920	121497414
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	19916001	13623598
Paired Opt. Dupes	18463	34172
% Dupes/100	0.3898	0.1121

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	51086508	121417759
Distinct Read Pairs	31172457	107806572
One Read Pair	18520607	95829671
Two Read Pairs	7839437	10543184
NRF = Distinct/Total	0.6102	0.8879
PBC1 = OnePair/Distinct	0.5941	0.8889
PBC2 = OnePair/TwoPair	2.3625	9.0893

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	62351838	215747632
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	62351838	215747632
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	62351838	215747632
Paired(QC-failed)	0	0
Read1	31175919	107873816
Read1(QC-failed)	0	0
Read2	31175919	107873816
Read2(QC-failed)	0	0
Properly Paired	62351838	215747632
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	62351838	215747632
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	108561
Np	0
N optimal	108561
N conservative	108561
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.	200
Corr. Est. Fragment Len.	0.1544
Phantom Peak	50
Corr. Phantom Peak	0.1578
Argmin. Corr.	1500
Min. Corr.	0.1475
NSC	1.0464
RSC	0.6679

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	0.3134

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	0.2291
AUC	0.4937
CHANCE divergence	0.1238
Elbow Point	0.0000
JS Distance	0.7038
Synthetic AUC	0.5022
Synthetic Elbow Point	0.2795
Synthetic JS Distance	0.3611