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Report generated at 2020-06-06 02:25:26

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	112518812	139413336
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	110752297	137076202
Mapped(QC-failed)	0	0
% Mapped	98.4300	98.3200
Paired	112518812	139413336
Paired(QC-failed)	0	0
Read1	56259406	69706668
Read1(QC-failed)	0	0
Read2	56259406	69706668
Read2(QC-failed)	0	0
Properly Paired	109881161	135724007
Properly Paired(QC-failed)	0	0
% Properly Paired	97.6600	97.3500
With itself	110444887	136521817
With itself(QC-failed)	0	0
Singletons	307410	554385
Singletons(QC-failed)	0	0
% Singleton	0.2700	0.4000
Diff. Chroms	71874	331576
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	49713346	59910556
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	14029694	3644145
Paired Opt. Dupes	2632	3362
% Dupes/100	0.2822	0.0608

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49712887	59868704
Distinct Read Pairs	35683331	56228098
One Read Pair	25126136	52787644
Two Read Pairs	7862651	3261892
NRF = Distinct/Total	0.7178	0.9392
PBC1 = OnePair/Distinct	0.7041	0.9388
PBC2 = OnePair/TwoPair	3.1956	16.1831

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	71367304	112532822
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	71367304	112532822
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	71367304	112532822
Paired(QC-failed)	0	0
Read1	35683652	56266411
Read1(QC-failed)	0	0
Read2	35683652	56266411
Read2(QC-failed)	0	0
Properly Paired	71367304	112532822
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	71367304	112532822
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	161757
Np	0
N optimal	161757
N conservative	161757
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.	165
Corr. Est. Fragment Len.	0.2305
Phantom Peak	50
Corr. Phantom Peak	0.2192
Argmin. Corr.	1500
Min. Corr.	0.1950
NSC	1.1820
RSC	1.4656

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	0.5141

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	0.1246
AUC	0.4952
CHANCE divergence	0.2622
Elbow Point	0.0000
JS Distance	0.7692
Synthetic AUC	0.4979
Synthetic Elbow Point	0.3932
Synthetic JS Distance	0.5141