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Report generated at 2020-06-06 00:01:10

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	131818224	78851830
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	127174747	77692986
Mapped(QC-failed)	0	0
% Mapped	96.4800	98.5300
Paired	131818224	78851830
Paired(QC-failed)	0	0
Read1	65909112	39425915
Read1(QC-failed)	0	0
Read2	65909112	39425915
Read2(QC-failed)	0	0
Properly Paired	125491558	77090443
Properly Paired(QC-failed)	0	0
% Properly Paired	95.2000	97.7700
With itself	126189641	77409309
With itself(QC-failed)	0	0
Singletons	985106	283677
Singletons(QC-failed)	0	0
% Singleton	0.7500	0.3600
Diff. Chroms	140476	84424
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	51448674	33992900
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	16754486	1011032
Paired Opt. Dupes	4818	3298
% Dupes/100	0.3257	0.0297

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	51446332	33975372
Distinct Read Pairs	34692559	32964969
One Read Pair	24889215	31985424
Two Read Pairs	5958809	949817
NRF = Distinct/Total	0.6743	0.9703
PBC1 = OnePair/Distinct	0.7174	0.9703
PBC2 = OnePair/TwoPair	4.1769	33.6754

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	69388376	65963736
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	69388376	65963736
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	69388376	65963736
Paired(QC-failed)	0	0
Read1	34694188	32981868
Read1(QC-failed)	0	0
Read2	34694188	32981868
Read2(QC-failed)	0	0
Properly Paired	69388376	65963736
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	69388376	65963736
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	46829
Np	0
N optimal	46829
N conservative	46829
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.	0.1667
Phantom Peak	50
Corr. Phantom Peak	0.1990
Argmin. Corr.	1500
Min. Corr.	0.1554
NSC	1.0729
RSC	0.2597

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	0.0294

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	0.2926
AUC	0.4951
CHANCE divergence	0.1250
Elbow Point	0.0000
JS Distance	0.5340
Synthetic AUC	0.4959
Synthetic Elbow Point	0.0678
Synthetic JS Distance	0.2491