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Report generated at 2020-05-26 11:11:43

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	146898058	78085830
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	145439002	76610347
Mapped(QC-failed)	0	0
% Mapped	99.0100	98.1100
Paired	146898058	78085830
Paired(QC-failed)	0	0
Read1	73449029	39042915
Read1(QC-failed)	0	0
Read2	73449029	39042915
Read2(QC-failed)	0	0
Properly Paired	144146925	74378590
Properly Paired(QC-failed)	0	0
% Properly Paired	98.1300	95.2500
With itself	144441561	75950585
With itself(QC-failed)	0	0
Singletons	997441	659762
Singletons(QC-failed)	0	0
% Singleton	0.6800	0.8400
Diff. Chroms	53712	90080
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	66870574	32826215
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	797202	205201
Paired Opt. Dupes	3486	1517
% Dupes/100	0.0119	0.0063

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	66826892	32750640
Distinct Read Pairs	66036154	32567543
One Read Pair	65256173	32390569
Two Read Pairs	769796	174492
NRF = Distinct/Total	0.9882	0.9944
PBC1 = OnePair/Distinct	0.9882	0.9946
PBC2 = OnePair/TwoPair	84.7707	185.6278

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	132146744	65242028
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	132146744	65242028
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	132146744	65242028
Paired(QC-failed)	0	0
Read1	66073372	32621014
Read1(QC-failed)	0	0
Read2	66073372	32621014
Read2(QC-failed)	0	0
Properly Paired	132146744	65242028
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	132146744	65242028
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	197325
Np	0
N optimal	197325
N conservative	197325
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.	150
Corr. Est. Fragment Len.	0.1759
Phantom Peak	50
Corr. Phantom Peak	0.1744
Argmin. Corr.	1500
Min. Corr.	0.1701
NSC	1.0343
RSC	1.3597

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	0.2179

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	0.2561
AUC	0.4965
CHANCE divergence	0.1030
Elbow Point	0.0000
JS Distance	0.6662
Synthetic AUC	0.5036
Synthetic Elbow Point	0.1511
Synthetic JS Distance	0.3192