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Report generated at 2020-05-13 08:04:23

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	60351910	55554290
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	58327840	53234328
Mapped(QC-failed)	0	0
% Mapped	96.6500	95.8200
Paired	60351910	55554290
Paired(QC-failed)	0	0
Read1	30175955	27777145
Read1(QC-failed)	0	0
Read2	30175955	27777145
Read2(QC-failed)	0	0
Properly Paired	56382921	46813080
Properly Paired(QC-failed)	0	0
% Properly Paired	93.4200	84.2700
With itself	57590572	52018273
With itself(QC-failed)	0	0
Singletons	737268	1216055
Singletons(QC-failed)	0	0
% Singleton	1.2200	2.1900
Diff. Chroms	913181	3541644
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	25443204	19892586
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	169060	222592
Paired Opt. Dupes	3180	2281
% Dupes/100	0.0066	0.0112

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	25443043	19890387
Distinct Read Pairs	25273984	19667823
One Read Pair	25105851	19447434
Two Read Pairs	167213	218233
NRF = Distinct/Total	0.9934	0.9888
PBC1 = OnePair/Distinct	0.9933	0.9888
PBC2 = OnePair/TwoPair	150.1429	89.1132

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	50548288	39339988
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	50548288	39339988
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	50548288	39339988
Paired(QC-failed)	0	0
Read1	25274144	19669994
Read1(QC-failed)	0	0
Read2	25274144	19669994
Read2(QC-failed)	0	0
Properly Paired	50548288	39339988
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	50548288	39339988
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	106639
Np	0
N optimal	106639
N conservative	106639
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.	265
Corr. Est. Fragment Len.	0.2012
Phantom Peak	50
Corr. Phantom Peak	0.1917
Argmin. Corr.	1500
Min. Corr.	0.1843
NSC	1.0919
RSC	2.2807

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	0.2247

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	0.1367
AUC	0.4942
CHANCE divergence	0.3997
Elbow Point	0.0000
JS Distance	0.6902
Synthetic AUC	0.4950
Synthetic Elbow Point	0.1214
Synthetic JS Distance	0.4101