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Report generated at 2020-05-02 11:54:28

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	52791204	45100544
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	30407024	42784977
Mapped(QC-failed)	0	0
% Mapped	57.6000	94.8700
Paired	52791204	45100544
Paired(QC-failed)	0	0
Read1	26395602	22550272
Read1(QC-failed)	0	0
Read2	26395602	22550272
Read2(QC-failed)	0	0
Properly Paired	28966205	34886479
Properly Paired(QC-failed)	0	0
% Properly Paired	54.8700	77.3500
With itself	29280386	41495730
With itself(QC-failed)	0	0
Singletons	1126638	1289247
Singletons(QC-failed)	0	0
% Singleton	2.1300	2.8600
Diff. Chroms	190856	4523333
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	13145246	13208684
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	262176	154251
Paired Opt. Dupes	2212	1783
% Dupes/100	0.0199	0.0117

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	13145057	13208667
Distinct Read Pairs	12882887	13054416
One Read Pair	12625024	12901708
Two Read Pairs	253612	151186
NRF = Distinct/Total	0.9801	0.9883
PBC1 = OnePair/Distinct	0.9800	0.9883
PBC2 = OnePair/TwoPair	49.7809	85.3367

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	25766140	26108866
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	25766140	26108866
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	25766140	26108866
Paired(QC-failed)	0	0
Read1	12883070	13054433
Read1(QC-failed)	0	0
Read2	12883070	13054433
Read2(QC-failed)	0	0
Properly Paired	25766140	26108866
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	25766140	26108866
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	24119
Np	0
N optimal	24119
N conservative	24119
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.	250
Corr. Est. Fragment Len.	0.4161
Phantom Peak	50
Corr. Phantom Peak	0.3504
Argmin. Corr.	1500
Min. Corr.	0.1538
NSC	2.7062
RSC	1.3344

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	0.4873

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	0.0744
AUC	0.4919
CHANCE divergence	0.5189
Elbow Point	0.0000
JS Distance	0.7966
Synthetic AUC	0.4969
Synthetic Elbow Point	0.4115
Synthetic JS Distance	0.5579