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Report generated at 2019-11-03 20:19:12

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	170081228	172537646
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	168091800	169623970
Mapped(QC-failed)	0	0
% Mapped	98.8300	98.3100
Paired	170081228	172537646
Paired(QC-failed)	0	0
Read1	85040614	86268823
Read1(QC-failed)	0	0
Read2	85040614	86268823
Read2(QC-failed)	0	0
Properly Paired	165931445	167189082
Properly Paired(QC-failed)	0	0
% Properly Paired	97.5600	96.9000
With itself	166829830	168209596
With itself(QC-failed)	0	0
Singletons	1261970	1414374
Singletons(QC-failed)	0	0
% Singleton	0.7400	0.8200
Diff. Chroms	231409	219888
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	74555717	73240672
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2663961	4951100
Paired Opt. Dupes	3431	3081
% Dupes/100	0.0357	0.0676

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	74554886	73151550
Distinct Read Pairs	71890966	68207516
One Read Pair	69294333	63530412
Two Read Pairs	2531249	4426047
NRF = Distinct/Total	0.9643	0.9324
PBC1 = OnePair/Distinct	0.9639	0.9314
PBC2 = OnePair/TwoPair	27.3756	14.3538

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	143783512	136579144
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	143783512	136579144
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	143783512	136579144
Paired(QC-failed)	0	0
Read1	71891756	68289572
Read1(QC-failed)	0	0
Read2	71891756	68289572
Read2(QC-failed)	0	0
Properly Paired	143783512	136579144
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	143783512	136579144
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	195991
Np	0
N optimal	195991
N conservative	195991
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.	160
Corr. Est. Fragment Len.	0.1714
Phantom Peak	50
Corr. Phantom Peak	0.1732
Argmin. Corr.	1500
Min. Corr.	0.1702
NSC	1.0073
RSC	0.4097

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	0.1774

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	0.2798
AUC	0.4966
CHANCE divergence	0.0962
Elbow Point	0.0000
JS Distance	0.5771
Synthetic AUC	0.5000
Synthetic Elbow Point	0.1541
Synthetic JS Distance	0.2868