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Report generated at 2020-07-15 04:44:43

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	190078752	103857894
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	188587278	102353291
Mapped(QC-failed)	0	0
% Mapped	99.2200	98.5500
Paired	190078752	103857894
Paired(QC-failed)	0	0
Read1	95039376	51928947
Read1(QC-failed)	0	0
Read2	95039376	51928947
Read2(QC-failed)	0	0
Properly Paired	180380871	100340149
Properly Paired(QC-failed)	0	0
% Properly Paired	94.9000	96.6100
With itself	187726065	101801899
With itself(QC-failed)	0	0
Singletons	861213	551392
Singletons(QC-failed)	0	0
% Singleton	0.4500	0.5300
Diff. Chroms	168050	131984
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	82465864	44269160
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3582271	406091
Paired Opt. Dupes	1543	1054
% Dupes/100	0.0434	0.0092

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	82464634	44267990
Distinct Read Pairs	78882392	43861911
One Read Pair	75565125	43470849
Two Read Pairs	3094815	382881
NRF = Distinct/Total	0.9566	0.9908
PBC1 = OnePair/Distinct	0.9579	0.9911
PBC2 = OnePair/TwoPair	24.4167	113.5362

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	157767186	87726138
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	157767186	87726138
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	157767186	87726138
Paired(QC-failed)	0	0
Read1	78883593	43863069
Read1(QC-failed)	0	0
Read2	78883593	43863069
Read2(QC-failed)	0	0
Properly Paired	157767186	87726138
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	157767186	87726138
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	274591
Np	0
N optimal	274591
N conservative	274591
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.	145
Corr. Est. Fragment Len.	0.1841
Phantom Peak	45
Corr. Phantom Peak	0.1765
Argmin. Corr.	1500
Min. Corr.	0.1732
NSC	1.0628
RSC	3.2331

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	0.3029

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	0.2027
AUC	0.4968
CHANCE divergence	0.1240
Elbow Point	0.0000
JS Distance	0.6528
Synthetic AUC	0.4969
Synthetic Elbow Point	0.2305
Synthetic JS Distance	0.4101