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Report generated at 2019-11-03 21:51:35

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	131385032	196869810
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	122687433	192216298
Mapped(QC-failed)	0	0
% Mapped	93.3800	97.6400
Paired	131385032	196869810
Paired(QC-failed)	0	0
Read1	65692516	98434905
Read1(QC-failed)	0	0
Read2	65692516	98434905
Read2(QC-failed)	0	0
Properly Paired	121086287	187412851
Properly Paired(QC-failed)	0	0
% Properly Paired	92.1600	95.2000
With itself	121937863	190908042
With itself(QC-failed)	0	0
Singletons	749570	1308256
Singletons(QC-failed)	0	0
% Singleton	0.5700	0.6600
Diff. Chroms	269266	1377453
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	52715795	83348574
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2106190	1654003
Paired Opt. Dupes	11070	15356
% Dupes/100	0.0400	0.0198

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	52711664	83232910
Distinct Read Pairs	50605647	81583711
One Read Pair	48569387	79958418
Two Read Pairs	1968740	1602927
NRF = Distinct/Total	0.9600	0.9802
PBC1 = OnePair/Distinct	0.9598	0.9801
PBC2 = OnePair/TwoPair	24.6703	49.8828

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	101219210	163389142
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	101219210	163389142
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	101219210	163389142
Paired(QC-failed)	0	0
Read1	50609605	81694571
Read1(QC-failed)	0	0
Read2	50609605	81694571
Read2(QC-failed)	0	0
Properly Paired	101219210	163389142
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	101219210	163389142
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	165213
Np	0
N optimal	165213
N conservative	165213
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.	140
Corr. Est. Fragment Len.	0.1810
Phantom Peak	50
Corr. Phantom Peak	0.1955
Argmin. Corr.	1500
Min. Corr.	0.1747
NSC	1.0362
RSC	0.3039

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	0.1474

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	0.2941
AUC	0.4959
CHANCE divergence	0.1008
Elbow Point	0.0000
JS Distance	0.5855
Synthetic AUC	0.5046
Synthetic Elbow Point	0.1399
Synthetic JS Distance	0.2561