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Report generated at 2020-05-04 01:36:40

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	171900840	137038710
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	160444497	132965142
Mapped(QC-failed)	0	0
% Mapped	93.3400	97.0300
Paired	171900840	137038710
Paired(QC-failed)	0	0
Read1	85950420	68519355
Read1(QC-failed)	0	0
Read2	85950420	68519355
Read2(QC-failed)	0	0
Properly Paired	157861320	130403765
Properly Paired(QC-failed)	0	0
% Properly Paired	91.8300	95.1600
With itself	159232650	132147488
With itself(QC-failed)	0	0
Singletons	1211847	817654
Singletons(QC-failed)	0	0
% Singleton	0.7000	0.6000
Diff. Chroms	593130	1017994
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	67507464	56489373
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	465411	246609
Paired Opt. Dupes	1021	1947
% Dupes/100	0.0069	0.0044

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	67499390	56440954
Distinct Read Pairs	67034039	56195118
One Read Pair	66572606	55950441
Two Read Pairs	457585	243541
NRF = Distinct/Total	0.9931	0.9956
PBC1 = OnePair/Distinct	0.9931	0.9956
PBC2 = OnePair/TwoPair	145.4869	229.7373

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	134084106	112485528
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	134084106	112485528
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	134084106	112485528
Paired(QC-failed)	0	0
Read1	67042053	56242764
Read1(QC-failed)	0	0
Read2	67042053	56242764
Read2(QC-failed)	0	0
Properly Paired	134084106	112485528
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	134084106	112485528
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	70960
Np	0
N optimal	70960
N conservative	70960
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.	105
Corr. Est. Fragment Len.	0.1851
Phantom Peak	50
Corr. Phantom Peak	0.2093
Argmin. Corr.	1500
Min. Corr.	0.1772
NSC	1.0445
RSC	0.2465

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	0.0399

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	0.3014
AUC	0.4965
CHANCE divergence	0.0937
Elbow Point	0.0000
JS Distance	0.5674
Synthetic AUC	0.5058
Synthetic Elbow Point	0.0311
Synthetic JS Distance	0.2502