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Report generated at 2020-05-10 14:20:55

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	70743588	94394890
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	66776008	90679650
Mapped(QC-failed)	0	0
% Mapped	94.3900	96.0600
Paired	70743588	94394890
Paired(QC-failed)	0	0
Read1	35371794	47197445
Read1(QC-failed)	0	0
Read2	35371794	47197445
Read2(QC-failed)	0	0
Properly Paired	64336775	85747226
Properly Paired(QC-failed)	0	0
% Properly Paired	90.9400	90.8400
With itself	65260457	88391054
With itself(QC-failed)	0	0
Singletons	1515551	2288596
Singletons(QC-failed)	0	0
% Singleton	2.1400	2.4200
Diff. Chroms	612738	1671322
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	27192163	36214131
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	180084	344208
Paired Opt. Dupes	1823	1746
% Dupes/100	0.0066	0.0095

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	27191339	36209957
Distinct Read Pairs	27011257	35865787
One Read Pair	26832250	35524443
Two Read Pairs	177941	338545
NRF = Distinct/Total	0.9934	0.9905
PBC1 = OnePair/Distinct	0.9934	0.9905
PBC2 = OnePair/TwoPair	150.7930	104.9327

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	54024158	71739846
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	54024158	71739846
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	54024158	71739846
Paired(QC-failed)	0	0
Read1	27012079	35869923
Read1(QC-failed)	0	0
Read2	27012079	35869923
Read2(QC-failed)	0	0
Properly Paired	54024158	71739846
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	54024158	71739846
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	174198
Np	0
N optimal	174198
N conservative	174198
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.	220
Corr. Est. Fragment Len.	0.1993
Phantom Peak	50
Corr. Phantom Peak	0.2033
Argmin. Corr.	1500
Min. Corr.	0.1864
NSC	1.0693
RSC	0.7671

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	0.3879

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	0.1600
AUC	0.4944
CHANCE divergence	0.2460
Elbow Point	0.0000
JS Distance	0.7213
Synthetic AUC	0.4983
Synthetic Elbow Point	0.2212
Synthetic JS Distance	0.4329