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Report generated at 2019-10-27 14:47:14

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	304382810	195514228
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	293162371	192553965
Mapped(QC-failed)	0	0
% Mapped	96.3100	98.4900
Paired	304382810	195514228
Paired(QC-failed)	0	0
Read1	152191405	97757114
Read1(QC-failed)	0	0
Read2	152191405	97757114
Read2(QC-failed)	0	0
Properly Paired	280765648	184591444
Properly Paired(QC-failed)	0	0
% Properly Paired	92.2400	94.4100
With itself	287724713	190690270
With itself(QC-failed)	0	0
Singletons	5437658	1863695
Singletons(QC-failed)	0	0
% Singleton	1.7900	0.9500
Diff. Chroms	2409345	4309653
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	91388877	77004602
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	10772780	6090607
Paired Opt. Dupes	20402	12922
% Dupes/100	0.1179	0.0791

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	91388000	76983195
Distinct Read Pairs	80615324	70894296
One Read Pair	70916111	65158036
Two Read Pairs	8739452	5405511
NRF = Distinct/Total	0.8821	0.9209
PBC1 = OnePair/Distinct	0.8797	0.9191
PBC2 = OnePair/TwoPair	8.1145	12.0540

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	161232194	141827990
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	161232194	141827990
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	161232194	141827990
Paired(QC-failed)	0	0
Read1	80616097	70913995
Read1(QC-failed)	0	0
Read2	80616097	70913995
Read2(QC-failed)	0	0
Properly Paired	161232194	141827990
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	161232194	141827990
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	230447
Np	0
N optimal	230447
N conservative	230447
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.	145
Corr. Est. Fragment Len.	0.2113
Phantom Peak	50
Corr. Phantom Peak	0.2524
Argmin. Corr.	1500
Min. Corr.	0.1999
NSC	1.0570
RSC	0.2172

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	0.2902

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	0.2344
AUC	0.4961
CHANCE divergence	0.0994
Elbow Point	0.0000
JS Distance	0.6637
Synthetic AUC	0.4998
Synthetic Elbow Point	0.2394
Synthetic JS Distance	0.3602