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Report generated at 2019-10-26 18:57:36

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	127604876	265917970
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	119862538	247468185
Mapped(QC-failed)	0	0
% Mapped	93.9300	93.0600
Paired	127604876	265917970
Paired(QC-failed)	0	0
Read1	63802438	132958985
Read1(QC-failed)	0	0
Read2	63802438	132958985
Read2(QC-failed)	0	0
Properly Paired	113267475	230014508
Properly Paired(QC-failed)	0	0
% Properly Paired	88.7600	86.5000
With itself	114849946	235762666
With itself(QC-failed)	0	0
Singletons	5012592	11705519
Singletons(QC-failed)	0	0
% Singleton	3.9300	4.4000
Diff. Chroms	235628	1000428
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	47161951	94715746
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	27119249	28466270
Paired Opt. Dupes	3170	5233
% Dupes/100	0.5750	0.3005

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	47154379	94356916
Distinct Read Pairs	20039277	66005399
One Read Pair	7388828	44764253
Two Read Pairs	5302706	15674972
NRF = Distinct/Total	0.4250	0.6995
PBC1 = OnePair/Distinct	0.3687	0.6782
PBC2 = OnePair/TwoPair	1.3934	2.8558

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	40085404	132498952
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	40085404	132498952
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	40085404	132498952
Paired(QC-failed)	0	0
Read1	20042702	66249476
Read1(QC-failed)	0	0
Read2	20042702	66249476
Read2(QC-failed)	0	0
Properly Paired	40085404	132498952
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	40085404	132498952
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	80507
Np	0
N optimal	80507
N conservative	80507
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.	155
Corr. Est. Fragment Len.	0.1255
Phantom Peak	50
Corr. Phantom Peak	0.1306
Argmin. Corr.	1500
Min. Corr.	0.1216
NSC	1.0319
RSC	0.4286

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	0.1843

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	0.2285
AUC	0.4921
CHANCE divergence	0.1526
Elbow Point	0.0000
JS Distance	0.6634
Synthetic AUC	0.4984
Synthetic Elbow Point	0.2002
Synthetic JS Distance	0.3393