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Report generated at 2020-06-06 06:57:00

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	214211844	82773480
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	199323789	80507883
Mapped(QC-failed)	0	0
% Mapped	93.0500	97.2600
Paired	214211844	82773480
Paired(QC-failed)	0	0
Read1	107105922	41386740
Read1(QC-failed)	0	0
Read2	107105922	41386740
Read2(QC-failed)	0	0
Properly Paired	197352844	79812054
Properly Paired(QC-failed)	0	0
% Properly Paired	92.1300	96.4200
With itself	198054754	80154095
With itself(QC-failed)	0	0
Singletons	1269035	353788
Singletons(QC-failed)	0	0
% Singleton	0.5900	0.4300
Diff. Chroms	226612	116599
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	88117678	35608364
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	24103573	3238646
Paired Opt. Dupes	23965	8047
% Dupes/100	0.2735	0.0910

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	88114125	35575289
Distinct Read Pairs	64011495	32339485
One Read Pair	46106515	29414677
Two Read Pairs	13243599	2647683
NRF = Distinct/Total	0.7265	0.9090
PBC1 = OnePair/Distinct	0.7203	0.9096
PBC2 = OnePair/TwoPair	3.4814	11.1096

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	128028210	64739436
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	128028210	64739436
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	128028210	64739436
Paired(QC-failed)	0	0
Read1	64014105	32369718
Read1(QC-failed)	0	0
Read2	64014105	32369718
Read2(QC-failed)	0	0
Properly Paired	128028210	64739436
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	128028210	64739436
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	86777
Np	0
N optimal	86777
N conservative	86777
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.	130
Corr. Est. Fragment Len.	0.1725
Phantom Peak	50
Corr. Phantom Peak	0.1820
Argmin. Corr.	1500
Min. Corr.	0.1664
NSC	1.0363
RSC	0.3876

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	0.0814

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	0.2944
AUC	0.4964
CHANCE divergence	0.1027
Elbow Point	0.0000
JS Distance	0.5687
Synthetic AUC	0.5002
Synthetic Elbow Point	0.0693
Synthetic JS Distance	0.2610