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Report generated at 2020-11-27 18:27:06

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	101882850	193594802
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	99667327	187969057
Mapped(QC-failed)	0	0
% Mapped	97.8300	97.0900
Paired	101882850	193594802
Paired(QC-failed)	0	0
Read1	50941425	96797401
Read1(QC-failed)	0	0
Read2	50941425	96797401
Read2(QC-failed)	0	0
Properly Paired	98098246	184287983
Properly Paired(QC-failed)	0	0
% Properly Paired	96.2900	95.1900
With itself	98452721	185784698
With itself(QC-failed)	0	0
Singletons	1214606	2184359
Singletons(QC-failed)	0	0
% Singleton	1.1900	1.1300
Diff. Chroms	175806	610670
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	44635128	78211821
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	800687	539110
Paired Opt. Dupes	4987	19807
% Dupes/100	0.0179	0.0069

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	44621543	77646644
Distinct Read Pairs	43821104	77172156
One Read Pair	43032727	76701136
Two Read Pairs	776464	467668
NRF = Distinct/Total	0.9821	0.9939
PBC1 = OnePair/Distinct	0.9820	0.9939
PBC2 = OnePair/TwoPair	55.4214	164.0077

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	87668882	155345422
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	87668882	155345422
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	87668882	155345422
Paired(QC-failed)	0	0
Read1	43834441	77672711
Read1(QC-failed)	0	0
Read2	43834441	77672711
Read2(QC-failed)	0	0
Properly Paired	87668882	155345422
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	87668882	155345422
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	119030
Np	0
N optimal	119030
N conservative	119030
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.	180
Corr. Est. Fragment Len.	0.2347
Phantom Peak	50
Corr. Phantom Peak	0.2242
Argmin. Corr.	1500
Min. Corr.	0.1926
NSC	1.2185
RSC	1.3300

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	0.4492

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	0.1736
AUC	0.4956
CHANCE divergence	0.1178
Elbow Point	0.0000
JS Distance	0.7978
Synthetic AUC	0.5080
Synthetic Elbow Point	0.3874
Synthetic JS Distance	0.4764