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Report generated at 2020-07-09 18:44:38

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	63372320	146003154
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	60874444	143950255
Mapped(QC-failed)	0	0
% Mapped	96.0600	98.5900
Paired	63372320	146003154
Paired(QC-failed)	0	0
Read1	31686160	73001577
Read1(QC-failed)	0	0
Read2	31686160	73001577
Read2(QC-failed)	0	0
Properly Paired	60413890	139355986
Properly Paired(QC-failed)	0	0
% Properly Paired	95.3300	95.4500
With itself	60598753	143134940
With itself(QC-failed)	0	0
Singletons	275691	815315
Singletons(QC-failed)	0	0
% Singleton	0.4400	0.5600
Diff. Chroms	26225	200467
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	27668259	61294235
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2569326	434896
Paired Opt. Dupes	1517	3707
% Dupes/100	0.0929	0.0071

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	27637008	61180783
Distinct Read Pairs	25072426	60780225
One Read Pair	22812307	60396899
Two Read Pairs	2041353	377062
NRF = Distinct/Total	0.9072	0.9935
PBC1 = OnePair/Distinct	0.9099	0.9937
PBC2 = OnePair/TwoPair	11.1751	160.1776

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	50197866	121718678
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	50197866	121718678
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	50197866	121718678
Paired(QC-failed)	0	0
Read1	25098933	60859339
Read1(QC-failed)	0	0
Read2	25098933	60859339
Read2(QC-failed)	0	0
Properly Paired	50197866	121718678
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	50197866	121718678
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	74649
Np	0
N optimal	74649
N conservative	74649
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.	160
Corr. Est. Fragment Len.	0.2418
Phantom Peak	55
Corr. Phantom Peak	0.1856
Argmin. Corr.	1500
Min. Corr.	0.1519
NSC	1.5917
RSC	2.6687

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	0.4064

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	0.1766
AUC	0.4943
CHANCE divergence	0.1438
Elbow Point	0.0000
JS Distance	0.7916
Synthetic AUC	0.4982
Synthetic Elbow Point	0.3876
Synthetic JS Distance	0.4706