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Report generated at 2019-10-13 03:24:44

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	104858348	115682520
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	98315466	110134967
Mapped(QC-failed)	0	0
% Mapped	93.7600	95.2000
Paired	104858348	115682520
Paired(QC-failed)	0	0
Read1	52429174	57841260
Read1(QC-failed)	0	0
Read2	52429174	57841260
Read2(QC-failed)	0	0
Properly Paired	92069973	104877577
Properly Paired(QC-failed)	0	0
% Properly Paired	87.8000	90.6600
With itself	92684459	106096677
With itself(QC-failed)	0	0
Singletons	5631007	4038290
Singletons(QC-failed)	0	0
% Singleton	5.3700	3.4900
Diff. Chroms	367773	752647
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	37267369	44143515
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	11552190	1315729
Paired Opt. Dupes	2906	4867
% Dupes/100	0.3100	0.0298

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	37266584	44113008
Distinct Read Pairs	25714615	42798457
One Read Pair	17620518	41528318
Two Read Pairs	5670911	1233455
NRF = Distinct/Total	0.6900	0.9702
PBC1 = OnePair/Distinct	0.6852	0.9703
PBC2 = OnePair/TwoPair	3.1072	33.6683

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	51430358	85655572
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	51430358	85655572
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	51430358	85655572
Paired(QC-failed)	0	0
Read1	25715179	42827786
Read1(QC-failed)	0	0
Read2	25715179	42827786
Read2(QC-failed)	0	0
Properly Paired	51430358	85655572
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	51430358	85655572
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	159201
Np	0
N optimal	159201
N conservative	159201
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.	125
Corr. Est. Fragment Len.	0.1520
Phantom Peak	50
Corr. Phantom Peak	0.1584
Argmin. Corr.	1500
Min. Corr.	0.1473
NSC	1.0319
RSC	0.4237

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	0.2677

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	0.2170
AUC	0.4943
CHANCE divergence	0.1466
Elbow Point	0.0000
JS Distance	0.6950
Synthetic AUC	0.5024
Synthetic Elbow Point	0.2181
Synthetic JS Distance	0.3652