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Report generated at 2019-10-13 14:18:11

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	193017994	90571450
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	182266211	89141373
Mapped(QC-failed)	0	0
% Mapped	94.4300	98.4200
Paired	193017994	90571450
Paired(QC-failed)	0	0
Read1	96508997	45285725
Read1(QC-failed)	0	0
Read2	96508997	45285725
Read2(QC-failed)	0	0
Properly Paired	180890049	88372908
Properly Paired(QC-failed)	0	0
% Properly Paired	93.7200	97.5700
With itself	181522417	88783529
With itself(QC-failed)	0	0
Singletons	743794	357844
Singletons(QC-failed)	0	0
% Singleton	0.3900	0.4000
Diff. Chroms	141590	165137
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	78530971	39015967
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	15997419	627860
Paired Opt. Dupes	7549	3635
% Dupes/100	0.2037	0.0161

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	78529560	38965090
Distinct Read Pairs	62532390	38338878
One Read Pair	49690940	37724707
Two Read Pairs	10259338	603360
NRF = Distinct/Total	0.7963	0.9839
PBC1 = OnePair/Distinct	0.7946	0.9840
PBC2 = OnePair/TwoPair	4.8435	62.5244

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	125067104	76776214
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	125067104	76776214
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	125067104	76776214
Paired(QC-failed)	0	0
Read1	62533552	38388107
Read1(QC-failed)	0	0
Read2	62533552	38388107
Read2(QC-failed)	0	0
Properly Paired	125067104	76776214
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	125067104	76776214
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	121584
Np	0
N optimal	121584
N conservative	121584
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.	210
Corr. Est. Fragment Len.	0.1728
Phantom Peak	50
Corr. Phantom Peak	0.1813
Argmin. Corr.	1500
Min. Corr.	0.1686
NSC	1.0251
RSC	0.3337

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	0.0738

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	0.2979
AUC	0.4964
CHANCE divergence	0.1034
Elbow Point	0.0000
JS Distance	0.5316
Synthetic AUC	0.5055
Synthetic Elbow Point	0.0758
Synthetic JS Distance	0.2558