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Report generated at 2019-10-25 14:35:25

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	96987190	108051026
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	92858972	106769052
Mapped(QC-failed)	0	0
% Mapped	95.7400	98.8100
Paired	96987190	108051026
Paired(QC-failed)	0	0
Read1	48493595	54025513
Read1(QC-failed)	0	0
Read2	48493595	54025513
Read2(QC-failed)	0	0
Properly Paired	88819333	102974844
Properly Paired(QC-failed)	0	0
% Properly Paired	91.5800	95.3000
With itself	91169950	106137917
With itself(QC-failed)	0	0
Singletons	1689022	631135
Singletons(QC-failed)	0	0
% Singleton	1.7400	0.5800
Diff. Chroms	1028473	2007136
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	30283738	42899753
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1230514	909722
Paired Opt. Dupes	7967	7276
% Dupes/100	0.0406	0.0212

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	30279226	42859157
Distinct Read Pairs	29048876	41950736
One Read Pair	27871383	41057737
Two Read Pairs	1131590	878320
NRF = Distinct/Total	0.9594	0.9788
PBC1 = OnePair/Distinct	0.9595	0.9787
PBC2 = OnePair/TwoPair	24.6303	46.7458

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	58106448	83980062
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	58106448	83980062
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	58106448	83980062
Paired(QC-failed)	0	0
Read1	29053224	41990031
Read1(QC-failed)	0	0
Read2	29053224	41990031
Read2(QC-failed)	0	0
Properly Paired	58106448	83980062
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	58106448	83980062
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	205226
Np	0
N optimal	205226
N conservative	205226
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.	110
Corr. Est. Fragment Len.	0.2119
Phantom Peak	50
Corr. Phantom Peak	0.2563
Argmin. Corr.	1500
Min. Corr.	0.1999
NSC	1.0597
RSC	0.2119

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	0.2836

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	0.2139
AUC	0.4935
CHANCE divergence	0.1304
Elbow Point	0.0000
JS Distance	0.7062
Synthetic AUC	0.5002
Synthetic Elbow Point	0.2061
Synthetic JS Distance	0.3769