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Report generated at 2021-02-05 11:33:50

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	61762148	106653906
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	59525564	104801407
Mapped(QC-failed)	0	0
% Mapped	96.3800	98.2600
Paired	61762148	106653906
Paired(QC-failed)	0	0
Read1	30881074	53326953
Read1(QC-failed)	0	0
Read2	30881074	53326953
Read2(QC-failed)	0	0
Properly Paired	59091899	102958254
Properly Paired(QC-failed)	0	0
% Properly Paired	95.6800	96.5300
With itself	59280920	104098130
With itself(QC-failed)	0	0
Singletons	244644	703277
Singletons(QC-failed)	0	0
% Singleton	0.4000	0.6600
Diff. Chroms	18555	170230
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	27697696	44220133
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3749066	314126
Paired Opt. Dupes	34602	110501
% Dupes/100	0.1354	0.0071

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	27693057	44206086
Distinct Read Pairs	23944611	43892511
One Read Pair	20760932	43597064
Two Read Pairs	2764570	288605
NRF = Distinct/Total	0.8646	0.9929
PBC1 = OnePair/Distinct	0.8670	0.9933
PBC2 = OnePair/TwoPair	7.5096	151.0614

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	47897260	87812014
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	47897260	87812014
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	47897260	87812014
Paired(QC-failed)	0	0
Read1	23948630	43906007
Read1(QC-failed)	0	0
Read2	23948630	43906007
Read2(QC-failed)	0	0
Properly Paired	47897260	87812014
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	47897260	87812014
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	105433
Np	0
N optimal	105433
N conservative	105433
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.	0.3050
Phantom Peak	55
Corr. Phantom Peak	0.2139
Argmin. Corr.	1500
Min. Corr.	0.1401
NSC	2.1778
RSC	2.2353

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	0.6186

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	0.0863
AUC	0.4939
CHANCE divergence	0.3143
Elbow Point	0.0000
JS Distance	0.8666
Synthetic AUC	0.4950
Synthetic Elbow Point	0.4772
Synthetic JS Distance	0.6002