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Report generated at 2020-05-04 19:44:34

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	191945892	197624996
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	170581732	192713678
Mapped(QC-failed)	0	0
% Mapped	88.8700	97.5100
Paired	191945892	197624996
Paired(QC-failed)	0	0
Read1	95972946	98812498
Read1(QC-failed)	0	0
Read2	95972946	98812498
Read2(QC-failed)	0	0
Properly Paired	165273040	189183779
Properly Paired(QC-failed)	0	0
% Properly Paired	86.1000	95.7300
With itself	167825364	191730743
With itself(QC-failed)	0	0
Singletons	2756368	982935
Singletons(QC-failed)	0	0
% Singleton	1.4400	0.5000
Diff. Chroms	720550	1513270
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	60493825	82282989
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	673294	411217
Paired Opt. Dupes	2394	3070
% Dupes/100	0.0111	0.0050

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	60490071	82255330
Distinct Read Pairs	59816825	81844454
One Read Pair	59183193	81439605
Two Read Pairs	607692	399981
NRF = Distinct/Total	0.9889	0.9950
PBC1 = OnePair/Distinct	0.9894	0.9951
PBC2 = OnePair/TwoPair	97.3901	203.6087

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	119641062	163743544
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	119641062	163743544
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	119641062	163743544
Paired(QC-failed)	0	0
Read1	59820531	81871772
Read1(QC-failed)	0	0
Read2	59820531	81871772
Read2(QC-failed)	0	0
Properly Paired	119641062	163743544
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	119641062	163743544
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	267886
Np	0
N optimal	267886
N conservative	267886
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.	125
Corr. Est. Fragment Len.	0.2115
Phantom Peak	50
Corr. Phantom Peak	0.2653
Argmin. Corr.	1500
Min. Corr.	0.1940
NSC	1.0900
RSC	0.2452

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	0.2901

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	0.2342
AUC	0.4963
CHANCE divergence	0.1038
Elbow Point	0.0000
JS Distance	0.6697
Synthetic AUC	0.4992
Synthetic Elbow Point	0.2045
Synthetic JS Distance	0.3603