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Report generated at 2019-11-04 01:35:17

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	177610694	194166736
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	150750059	188427054
Mapped(QC-failed)	0	0
% Mapped	84.8800	97.0400
Paired	177610694	194166736
Paired(QC-failed)	0	0
Read1	88805347	97083368
Read1(QC-failed)	0	0
Read2	88805347	97083368
Read2(QC-failed)	0	0
Properly Paired	147457541	183258385
Properly Paired(QC-failed)	0	0
% Properly Paired	83.0200	94.3800
With itself	149519362	186937146
With itself(QC-failed)	0	0
Singletons	1230697	1489908
Singletons(QC-failed)	0	0
% Singleton	0.6900	0.7700
Diff. Chroms	247020	1235264
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	63805255	80987770
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2706454	1179794
Paired Opt. Dupes	8167	10644
% Dupes/100	0.0424	0.0146

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	63802478	80909491
Distinct Read Pairs	61096175	79732095
One Read Pair	58480967	78571982
Two Read Pairs	2527387	1145607
NRF = Distinct/Total	0.9576	0.9854
PBC1 = OnePair/Distinct	0.9572	0.9855
PBC2 = OnePair/TwoPair	23.1389	68.5855

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	122197602	159615952
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	122197602	159615952
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	122197602	159615952
Paired(QC-failed)	0	0
Read1	61098801	79807976
Read1(QC-failed)	0	0
Read2	61098801	79807976
Read2(QC-failed)	0	0
Properly Paired	122197602	159615952
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	122197602	159615952
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	156613
Np	0
N optimal	156613
N conservative	156613
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.	120
Corr. Est. Fragment Len.	0.1814
Phantom Peak	50
Corr. Phantom Peak	0.1999
Argmin. Corr.	1500
Min. Corr.	0.1757
NSC	1.0328
RSC	0.2375

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	0.1029

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	0.3125
AUC	0.4963
CHANCE divergence	0.0933
Elbow Point	0.0000
JS Distance	0.5609
Synthetic AUC	0.5004
Synthetic Elbow Point	0.0974
Synthetic JS Distance	0.2313