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Report generated at 2020-06-10 07:19:00

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	61907932	123436302
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	61444404	121216389
Mapped(QC-failed)	0	0
% Mapped	99.2500	98.2000
Paired	61907932	123436302
Paired(QC-failed)	0	0
Read1	30953966	61718151
Read1(QC-failed)	0	0
Read2	30953966	61718151
Read2(QC-failed)	0	0
Properly Paired	60989729	118424048
Properly Paired(QC-failed)	0	0
% Properly Paired	98.5200	95.9400
With itself	61113094	120225855
With itself(QC-failed)	0	0
Singletons	331310	990534
Singletons(QC-failed)	0	0
% Singleton	0.5400	0.8000
Diff. Chroms	17522	233679
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	28965391	52405522
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	478113	353361
Paired Opt. Dupes	2141	2501
% Dupes/100	0.0165	0.0067

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	28958174	52322111
Distinct Read Pairs	28480296	51995463
One Read Pair	28031845	51683877
Two Read Pairs	425229	305227
NRF = Distinct/Total	0.9835	0.9938
PBC1 = OnePair/Distinct	0.9843	0.9940
PBC2 = OnePair/TwoPair	65.9218	169.3293

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	56974556	104104322
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	56974556	104104322
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	56974556	104104322
Paired(QC-failed)	0	0
Read1	28487278	52052161
Read1(QC-failed)	0	0
Read2	28487278	52052161
Read2(QC-failed)	0	0
Properly Paired	56974556	104104322
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	56974556	104104322
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	110105
Np	0
N optimal	110105
N conservative	110105
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.	0.2421
Phantom Peak	45
Corr. Phantom Peak	0.2143
Argmin. Corr.	1500
Min. Corr.	0.1884
NSC	1.2852
RSC	2.0762

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	0.5327

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	0.1222
AUC	0.4946
CHANCE divergence	0.2252
Elbow Point	0.0000
JS Distance	0.8173
Synthetic AUC	0.5070
Synthetic Elbow Point	0.4162
Synthetic JS Distance	0.5365