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Report generated at 2021-10-21 08:20:54

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	173926054	215916580
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	168916938	212163850
Mapped(QC-failed)	0	0
% Mapped	97.1200	98.2600
Paired	173926054	215916580
Paired(QC-failed)	0	0
Read1	86963027	107958290
Read1(QC-failed)	0	0
Read2	86963027	107958290
Read2(QC-failed)	0	0
Properly Paired	164489899	203494730
Properly Paired(QC-failed)	0	0
% Properly Paired	94.5700	94.2500
With itself	166590054	210124486
With itself(QC-failed)	0	0
Singletons	2326884	2039364
Singletons(QC-failed)	0	0
% Singleton	1.3400	0.9400
Diff. Chroms	1390611	4820338
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	71346778	84863940
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	5336754	4207317
Paired Opt. Dupes	31868	26763
% Dupes/100	0.0748	0.0496

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	71339235	84737544
Distinct Read Pairs	66003022	80538942
One Read Pair	60998868	76496172
Two Read Pairs	4691071	3894193
NRF = Distinct/Total	0.9252	0.9505
PBC1 = OnePair/Distinct	0.9242	0.9498
PBC2 = OnePair/TwoPair	13.0032	19.6437

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	132020048	161313246
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	132020048	161313246
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	132020048	161313246
Paired(QC-failed)	0	0
Read1	66010024	80656623
Read1(QC-failed)	0	0
Read2	66010024	80656623
Read2(QC-failed)	0	0
Properly Paired	132020048	161313246
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	132020048	161313246
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	135900
Np	0
N optimal	135900
N conservative	135900
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.	215
Corr. Est. Fragment Len.	0.1857
Phantom Peak	50
Corr. Phantom Peak	0.1889
Argmin. Corr.	1500
Min. Corr.	0.1768
NSC	1.0503
RSC	0.7403

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	0.4446

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	0.2116
AUC	0.4957
CHANCE divergence	0.1069
Elbow Point	0.0000
JS Distance	0.7859
Synthetic AUC	0.5026
Synthetic Elbow Point	0.3108
Synthetic JS Distance	0.4043