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Report generated at 2021-02-06 03:55:41

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	128553632	136919114
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	127126347	134757903
Mapped(QC-failed)	0	0
% Mapped	98.8900	98.4200
Paired	128553632	136919114
Paired(QC-failed)	0	0
Read1	64276816	68459557
Read1(QC-failed)	0	0
Read2	64276816	68459557
Read2(QC-failed)	0	0
Properly Paired	118694234	131935292
Properly Paired(QC-failed)	0	0
% Properly Paired	92.3300	96.3600
With itself	126438194	133937802
With itself(QC-failed)	0	0
Singletons	688153	820101
Singletons(QC-failed)	0	0
% Singleton	0.5400	0.6000
Diff. Chroms	200782	184333
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	51587923	57012328
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	659898	408353
Paired Opt. Dupes	6830	8386
% Dupes/100	0.0128	0.0072

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	51571582	56995712
Distinct Read Pairs	50912505	56588428
One Read Pair	50266749	56205893
Two Read Pairs	634847	372834
NRF = Distinct/Total	0.9872	0.9929
PBC1 = OnePair/Distinct	0.9873	0.9932
PBC2 = OnePair/TwoPair	79.1793	150.7531

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	101856050	113207950
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	101856050	113207950
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	101856050	113207950
Paired(QC-failed)	0	0
Read1	50928025	56603975
Read1(QC-failed)	0	0
Read2	50928025	56603975
Read2(QC-failed)	0	0
Properly Paired	101856050	113207950
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	101856050	113207950
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	205554
Np	0
N optimal	205554
N conservative	205554
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.	145
Corr. Est. Fragment Len.	0.1854
Phantom Peak	50
Corr. Phantom Peak	0.1864
Argmin. Corr.	1500
Min. Corr.	0.1774
NSC	1.0446
RSC	0.8807

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	0.1641

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	0.2304
AUC	0.4958
CHANCE divergence	0.1329
Elbow Point	0.0000
JS Distance	0.6060
Synthetic AUC	0.5039
Synthetic Elbow Point	0.1318
Synthetic JS Distance	0.3567