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Report generated at 2020-06-06 01:01:31

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	121185414	74925678
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	107243544	73334040
Mapped(QC-failed)	0	0
% Mapped	88.5000	97.8800
Paired	121185414	74925678
Paired(QC-failed)	0	0
Read1	60592707	37462839
Read1(QC-failed)	0	0
Read2	60592707	37462839
Read2(QC-failed)	0	0
Properly Paired	106439529	72502624
Properly Paired(QC-failed)	0	0
% Properly Paired	87.8300	96.7700
With itself	106813025	73039911
With itself(QC-failed)	0	0
Singletons	430519	294129
Singletons(QC-failed)	0	0
% Singleton	0.3600	0.3900
Diff. Chroms	69286	216939
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	49191365	32127407
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7899329	360854
Paired Opt. Dupes	2726	4136
% Dupes/100	0.1606	0.0112

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49183454	31804933
Distinct Read Pairs	41285416	31477794
One Read Pair	34635345	31163507
Two Read Pairs	5585493	307462
NRF = Distinct/Total	0.8394	0.9897
PBC1 = OnePair/Distinct	0.8389	0.9900
PBC2 = OnePair/TwoPair	6.2009	101.3573

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	82584072	63533106
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	82584072	63533106
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	82584072	63533106
Paired(QC-failed)	0	0
Read1	41292036	31766553
Read1(QC-failed)	0	0
Read2	41292036	31766553
Read2(QC-failed)	0	0
Properly Paired	82584072	63533106
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	82584072	63533106
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	153152
Np	0
N optimal	153152
N conservative	153152
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.	140
Corr. Est. Fragment Len.	0.2038
Phantom Peak	50
Corr. Phantom Peak	0.1998
Argmin. Corr.	1500
Min. Corr.	0.1753
NSC	1.1625
RSC	1.1644

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	0.3697

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	0.1914
AUC	0.4955
CHANCE divergence	0.1189
Elbow Point	0.0000
JS Distance	0.7582
Synthetic AUC	0.4981
Synthetic Elbow Point	0.3026
Synthetic JS Distance	0.4359