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Report generated at 2020-06-05 14:37:29

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	70409804	65898052
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	68163965	64625224
Mapped(QC-failed)	0	0
% Mapped	96.8100	98.0700
Paired	70409804	65898052
Paired(QC-failed)	0	0
Read1	35204902	32949026
Read1(QC-failed)	0	0
Read2	35204902	32949026
Read2(QC-failed)	0	0
Properly Paired	67092534	63833486
Properly Paired(QC-failed)	0	0
% Properly Paired	95.2900	96.8700
With itself	67453297	64118603
With itself(QC-failed)	0	0
Singletons	710668	506621
Singletons(QC-failed)	0	0
% Singleton	1.0100	0.7700
Diff. Chroms	44319	74019
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	30002668	28025050
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6883134	294266
Paired Opt. Dupes	2167	2128
% Dupes/100	0.2294	0.0105

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	29991107	27554999
Distinct Read Pairs	23110690	27340362
One Read Pair	17577781	27129504
Two Read Pairs	4415843	207820
NRF = Distinct/Total	0.7706	0.9922
PBC1 = OnePair/Distinct	0.7606	0.9923
PBC2 = OnePair/TwoPair	3.9806	130.5433

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	46239068	55461568
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	46239068	55461568
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	46239068	55461568
Paired(QC-failed)	0	0
Read1	23119534	27730784
Read1(QC-failed)	0	0
Read2	23119534	27730784
Read2(QC-failed)	0	0
Properly Paired	46239068	55461568
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	46239068	55461568
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	74530
Np	0
N optimal	74530
N conservative	74530
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.	180
Corr. Est. Fragment Len.	0.2208
Phantom Peak	50
Corr. Phantom Peak	0.2083
Argmin. Corr.	1500
Min. Corr.	0.1664
NSC	1.3275
RSC	1.2992

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	0.3411

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	0.1898
AUC	0.4940
CHANCE divergence	0.1498
Elbow Point	0.0000
JS Distance	0.7471
Synthetic AUC	0.5033
Synthetic Elbow Point	0.3218
Synthetic JS Distance	0.4373