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Report generated at 2020-05-13 13:10:39

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	66797778	78498540
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	60431133	74844187
Mapped(QC-failed)	0	0
% Mapped	90.4700	95.3400
Paired	66797778	78498540
Paired(QC-failed)	0	0
Read1	33398889	39249270
Read1(QC-failed)	0	0
Read2	33398889	39249270
Read2(QC-failed)	0	0
Properly Paired	57644017	67679938
Properly Paired(QC-failed)	0	0
% Properly Paired	86.3000	86.2200
With itself	59004869	72834832
With itself(QC-failed)	0	0
Singletons	1426264	2009355
Singletons(QC-failed)	0	0
% Singleton	2.1400	2.5600
Diff. Chroms	948960	3424690
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	25006056	28005715
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	294286	528129
Paired Opt. Dupes	2232	2652
% Dupes/100	0.0118	0.0189

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	25001818	28000939
Distinct Read Pairs	24707589	27472963
One Read Pair	24416375	26953277
Two Read Pairs	288228	511504
NRF = Distinct/Total	0.9882	0.9811
PBC1 = OnePair/Distinct	0.9882	0.9811
PBC2 = OnePair/TwoPair	84.7120	52.6942

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	49423540	54955172
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	49423540	54955172
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	49423540	54955172
Paired(QC-failed)	0	0
Read1	24711770	27477586
Read1(QC-failed)	0	0
Read2	24711770	27477586
Read2(QC-failed)	0	0
Properly Paired	49423540	54955172
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	49423540	54955172
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	108784
Np	0
N optimal	108784
N conservative	108784
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.	235
Corr. Est. Fragment Len.	0.2101
Phantom Peak	50
Corr. Phantom Peak	0.2047
Argmin. Corr.	1500
Min. Corr.	0.1928
NSC	1.0894
RSC	1.4495

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	0.2706

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	0.1222
AUC	0.4942
CHANCE divergence	0.4214
Elbow Point	0.0000
JS Distance	0.7162
Synthetic AUC	0.4956
Synthetic Elbow Point	0.1342
Synthetic JS Distance	0.4353