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Report generated at 2019-10-12 21:57:12

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	77399016	95805330
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	73875759	91174239
Mapped(QC-failed)	0	0
% Mapped	95.4500	95.1700
Paired	77399016	95805330
Paired(QC-failed)	0	0
Read1	38699508	47902665
Read1(QC-failed)	0	0
Read2	38699508	47902665
Read2(QC-failed)	0	0
Properly Paired	70800829	87029614
Properly Paired(QC-failed)	0	0
% Properly Paired	91.4800	90.8400
With itself	71329868	88132031
With itself(QC-failed)	0	0
Singletons	2545891	3042208
Singletons(QC-failed)	0	0
% Singleton	3.2900	3.1800
Diff. Chroms	267278	677774
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	29890437	36289675
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1596928	346498
Paired Opt. Dupes	3404	3852
% Dupes/100	0.0534	0.0095

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	29889435	36261516
Distinct Read Pairs	28292560	35915541
One Read Pair	26780041	35581631
Two Read Pairs	1433174	326616
NRF = Distinct/Total	0.9466	0.9905
PBC1 = OnePair/Distinct	0.9465	0.9907
PBC2 = OnePair/TwoPair	18.6858	108.9403

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	56587018	71886354
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	56587018	71886354
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	56587018	71886354
Paired(QC-failed)	0	0
Read1	28293509	35943177
Read1(QC-failed)	0	0
Read2	28293509	35943177
Read2(QC-failed)	0	0
Properly Paired	56587018	71886354
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	56587018	71886354
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	59365
Np	0
N optimal	59365
N conservative	59365
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.	0.1716
Phantom Peak	50
Corr. Phantom Peak	0.1808
Argmin. Corr.	1500
Min. Corr.	0.1681
NSC	1.0207
RSC	0.2761

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	0.0451

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	0.2962
AUC	0.4946
CHANCE divergence	0.1087
Elbow Point	0.0000
JS Distance	0.5603
Synthetic AUC	0.5070
Synthetic Elbow Point	0.0634
Synthetic JS Distance	0.2459