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Report generated at 2020-06-10 19:03:11

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	91428512	208397864
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	91049429	205001725
Mapped(QC-failed)	0	0
% Mapped	99.5900	98.3700
Paired	91428512	208397864
Paired(QC-failed)	0	0
Read1	45714256	104198932
Read1(QC-failed)	0	0
Read2	45714256	104198932
Read2(QC-failed)	0	0
Properly Paired	90777477	199305552
Properly Paired(QC-failed)	0	0
% Properly Paired	99.2900	95.6400
With itself	90835935	203636967
With itself(QC-failed)	0	0
Singletons	213494	1364758
Singletons(QC-failed)	0	0
% Singleton	0.2300	0.6500
Diff. Chroms	14951	299406
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	42715861	87961925
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2970068	1539621
Paired Opt. Dupes	1783	2337
% Dupes/100	0.0695	0.0175

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42712330	87957322
Distinct Read Pairs	39742353	86418077
One Read Pair	37676754	84991683
Two Read Pairs	1595899	1357144
NRF = Distinct/Total	0.9305	0.9825
PBC1 = OnePair/Distinct	0.9480	0.9835
PBC2 = OnePair/TwoPair	23.6085	62.6254

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	79491586	172844608
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	79491586	172844608
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	79491586	172844608
Paired(QC-failed)	0	0
Read1	39745793	86422304
Read1(QC-failed)	0	0
Read2	39745793	86422304
Read2(QC-failed)	0	0
Properly Paired	79491586	172844608
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	79491586	172844608
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	102324
Np	0
N optimal	102324
N conservative	102324
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.	165
Corr. Est. Fragment Len.	0.3269
Phantom Peak	55
Corr. Phantom Peak	0.2158
Argmin. Corr.	1500
Min. Corr.	0.1602
NSC	2.0399
RSC	2.9972

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	0.8052

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	0.0441
AUC	0.4954
CHANCE divergence	0.3817
Elbow Point	0.0000
JS Distance	0.9068
Synthetic AUC	0.5010
Synthetic Elbow Point	0.6350
Synthetic JS Distance	0.7139