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Report generated at 2022-09-02 12:31:47

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	149219918	65769896
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	140412992	64886900
Mapped(QC-failed)	0	0
% Mapped	94.1000	98.6600
Paired	149219918	65769896
Paired(QC-failed)	0	0
Read1	74609959	32884948
Read1(QC-failed)	0	0
Read2	74609959	32884948
Read2(QC-failed)	0	0
Properly Paired	139432364	64470476
Properly Paired(QC-failed)	0	0
% Properly Paired	93.4400	98.0200
With itself	139861592	64685111
With itself(QC-failed)	0	0
Singletons	551400	201789
Singletons(QC-failed)	0	0
% Singleton	0.3700	0.3100
Diff. Chroms	120659	65977
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	63759815	28526999
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	13401915	113439
Paired Opt. Dupes	6712	1566
% Dupes/100	0.2102	0.0040

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	63749886	28513550
Distinct Read Pairs	50349988	28400237
One Read Pair	39480387	28288484
Two Read Pairs	8771060	110529
NRF = Distinct/Total	0.7898	0.9960
PBC1 = OnePair/Distinct	0.7841	0.9961
PBC2 = OnePair/TwoPair	4.5012	255.9372

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	100715800	56827120
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	100715800	56827120
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	100715800	56827120
Paired(QC-failed)	0	0
Read1	50357900	28413560
Read1(QC-failed)	0	0
Read2	50357900	28413560
Read2(QC-failed)	0	0
Properly Paired	100715800	56827120
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	100715800	56827120
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	262788
Np	0
N optimal	262788
N conservative	262788
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.	205
Corr. Est. Fragment Len.	0.1733
Phantom Peak	50
Corr. Phantom Peak	0.1742
Argmin. Corr.	1500
Min. Corr.	0.1695
NSC	1.0224
RSC	0.8044

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	0.3792

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	0.2009
AUC	0.4959
CHANCE divergence	0.1143
Elbow Point	0.0000
JS Distance	0.7147
Synthetic AUC	0.5008
Synthetic Elbow Point	0.2403
Synthetic JS Distance	0.4098