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Report generated at 2020-05-13 14:05:40

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	68940840	78498540
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	60900725	74844187
Mapped(QC-failed)	0	0
% Mapped	88.3400	95.3400
Paired	68940840	78498540
Paired(QC-failed)	0	0
Read1	34470420	39249270
Read1(QC-failed)	0	0
Read2	34470420	39249270
Read2(QC-failed)	0	0
Properly Paired	55854825	67679938
Properly Paired(QC-failed)	0	0
% Properly Paired	81.0200	86.2200
With itself	58387893	72834832
With itself(QC-failed)	0	0
Singletons	2512832	2009355
Singletons(QC-failed)	0	0
% Singleton	3.6400	2.5600
Diff. Chroms	1104264	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	22261312	28005715
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	574731	528129
Paired Opt. Dupes	2331	2652
% Dupes/100	0.0258	0.0189

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	22254915	28000939
Distinct Read Pairs	21680362	27472963
One Read Pair	21118303	26953277
Two Read Pairs	549814	511504
NRF = Distinct/Total	0.9742	0.9811
PBC1 = OnePair/Distinct	0.9741	0.9811
PBC2 = OnePair/TwoPair	38.4099	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	43373162	54955172
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	43373162	54955172
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	43373162	54955172
Paired(QC-failed)	0	0
Read1	21686581	27477586
Read1(QC-failed)	0	0
Read2	21686581	27477586
Read2(QC-failed)	0	0
Properly Paired	43373162	54955172
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	43373162	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	81967
Np	0
N optimal	81967
N conservative	81967
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.	270
Corr. Est. Fragment Len.	0.2186
Phantom Peak	50
Corr. Phantom Peak	0.2322
Argmin. Corr.	1500
Min. Corr.	0.1950
NSC	1.1214
RSC	0.6365

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	0.1483

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	0.1607
AUC	0.4938
CHANCE divergence	0.3702
Elbow Point	0.0000
JS Distance	0.6505
Synthetic AUC	0.4960
Synthetic Elbow Point	0.0907
Synthetic JS Distance	0.3683