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Report generated at 2020-04-09 01:20:22

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	129563068	125060354
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	126896793	115723438
Mapped(QC-failed)	0	0
% Mapped	97.9400	92.5300
Paired	129563068	125060354
Paired(QC-failed)	0	0
Read1	64781534	62530177
Read1(QC-failed)	0	0
Read2	64781534	62530177
Read2(QC-failed)	0	0
Properly Paired	125449142	106455838
Properly Paired(QC-failed)	0	0
% Properly Paired	96.8200	85.1200
With itself	126080876	108232133
With itself(QC-failed)	0	0
Singletons	815917	7491305
Singletons(QC-failed)	0	0
% Singleton	0.6300	5.9900
Diff. Chroms	246362	1197687
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	55057808	42322259
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2257069	491414
Paired Opt. Dupes	3616	3358
% Dupes/100	0.0410	0.0116

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	55056447	42292180
Distinct Read Pairs	52799431	41801358
One Read Pair	50646313	41322447
Two Read Pairs	2063980	470042
NRF = Distinct/Total	0.9590	0.9884
PBC1 = OnePair/Distinct	0.9592	0.9885
PBC2 = OnePair/TwoPair	24.5382	87.9122

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	105601478	83661690
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	105601478	83661690
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	105601478	83661690
Paired(QC-failed)	0	0
Read1	52800739	41830845
Read1(QC-failed)	0	0
Read2	52800739	41830845
Read2(QC-failed)	0	0
Properly Paired	105601478	83661690
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	105601478	83661690
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	38202
Np	0
N optimal	38202
N conservative	38202
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.	110
Corr. Est. Fragment Len.	0.1752
Phantom Peak	50
Corr. Phantom Peak	0.1885
Argmin. Corr.	1500
Min. Corr.	0.1701
NSC	1.0300
RSC	0.2773

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	0.0381

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	0.3327
AUC	0.4960
CHANCE divergence	0.1004
Elbow Point	0.0000
JS Distance	0.5003
Synthetic AUC	0.5019
Synthetic Elbow Point	0.0507
Synthetic JS Distance	0.2002