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Report generated at 2021-02-05 13:22:43

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	53802814	136919114
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	51818958	134757903
Mapped(QC-failed)	0	0
% Mapped	96.3100	98.4200
Paired	53802814	136919114
Paired(QC-failed)	0	0
Read1	26901407	68459557
Read1(QC-failed)	0	0
Read2	26901407	68459557
Read2(QC-failed)	0	0
Properly Paired	51399758	131935292
Properly Paired(QC-failed)	0	0
% Properly Paired	95.5300	96.3600
With itself	51600816	133937802
With itself(QC-failed)	0	0
Singletons	218142	820101
Singletons(QC-failed)	0	0
% Singleton	0.4100	0.6000
Diff. Chroms	19305	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	24123487	57012328
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2537348	408353
Paired Opt. Dupes	19353	8386
% Dupes/100	0.1052	0.0072

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	24120285	56995712
Distinct Read Pairs	21583223	56588428
One Read Pair	19456841	56205893
Two Read Pairs	1867101	372834
NRF = Distinct/Total	0.8948	0.9929
PBC1 = OnePair/Distinct	0.9015	0.9932
PBC2 = OnePair/TwoPair	10.4209	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	43172278	113207950
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	43172278	113207950
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	43172278	113207950
Paired(QC-failed)	0	0
Read1	21586139	56603975
Read1(QC-failed)	0	0
Read2	21586139	56603975
Read2(QC-failed)	0	0
Properly Paired	43172278	113207950
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	43172278	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	92810
Np	0
N optimal	92810
N conservative	92810
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.	0.3482
Phantom Peak	55
Corr. Phantom Peak	0.2427
Argmin. Corr.	1500
Min. Corr.	0.1496
NSC	2.3269
RSC	2.1338

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	0.6461

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	0.0768
AUC	0.4936
CHANCE divergence	0.3512
Elbow Point	0.0000
JS Distance	0.8781
Synthetic AUC	0.5090
Synthetic Elbow Point	0.5136
Synthetic JS Distance	0.6189