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Report generated at 2020-07-07 23:45:50

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	137292782	180205796
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	135971303	177256107
Mapped(QC-failed)	0	0
% Mapped	99.0400	98.3600
Paired	137292782	180205796
Paired(QC-failed)	0	0
Read1	68646391	90102898
Read1(QC-failed)	0	0
Read2	68646391	90102898
Read2(QC-failed)	0	0
Properly Paired	134821572	170638517
Properly Paired(QC-failed)	0	0
% Properly Paired	98.2000	94.6900
With itself	135174021	176150891
With itself(QC-failed)	0	0
Singletons	797282	1105216
Singletons(QC-failed)	0	0
% Singleton	0.5800	0.6100
Diff. Chroms	42899	330969
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	62474121	75018779
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2500065	1307836
Paired Opt. Dupes	3746	2748
% Dupes/100	0.0400	0.0174

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	62457529	75016635
Distinct Read Pairs	59959215	73708883
One Read Pair	57568509	72495647
Two Read Pairs	2296758	1155222
NRF = Distinct/Total	0.9600	0.9826
PBC1 = OnePair/Distinct	0.9601	0.9835
PBC2 = OnePair/TwoPair	25.0651	62.7547

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	119948112	147421886
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	119948112	147421886
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	119948112	147421886
Paired(QC-failed)	0	0
Read1	59974056	73710943
Read1(QC-failed)	0	0
Read2	59974056	73710943
Read2(QC-failed)	0	0
Properly Paired	119948112	147421886
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	119948112	147421886
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	214662
Np	0
N optimal	214662
N conservative	214662
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.	155
Corr. Est. Fragment Len.	0.1869
Phantom Peak	55
Corr. Phantom Peak	0.1824
Argmin. Corr.	1500
Min. Corr.	0.1697
NSC	1.1014
RSC	1.3470

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	0.4790

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	0.1943
AUC	0.4963
CHANCE divergence	0.1070
Elbow Point	0.0000
JS Distance	0.7793
Synthetic AUC	0.4966
Synthetic Elbow Point	0.2940
Synthetic JS Distance	0.4311