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Report generated at 2020-05-10 19:38:39

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	67732554	49040330
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	48266954	43899885
Mapped(QC-failed)	0	0
% Mapped	71.2600	89.5200
Paired	67732554	49040330
Paired(QC-failed)	0	0
Read1	33866277	24520165
Read1(QC-failed)	0	0
Read2	33866277	24520165
Read2(QC-failed)	0	0
Properly Paired	35564968	30373686
Properly Paired(QC-failed)	0	0
% Properly Paired	52.5100	61.9400
With itself	44710136	41523513
With itself(QC-failed)	0	0
Singletons	3556818	2376372
Singletons(QC-failed)	0	0
% Singleton	5.2500	4.8500
Diff. Chroms	4528695	7654539
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	11585309	10159811
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	266930	264224
Paired Opt. Dupes	1139	1355
% Dupes/100	0.0230	0.0260

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	11581826	10158782
Distinct Read Pairs	11314959	9894586
One Read Pair	11053501	9636269
Two Read Pairs	256149	252589
NRF = Distinct/Total	0.9770	0.9740
PBC1 = OnePair/Distinct	0.9769	0.9739
PBC2 = OnePair/TwoPair	43.1526	38.1500

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	22636758	19791174
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	22636758	19791174
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	22636758	19791174
Paired(QC-failed)	0	0
Read1	11318379	9895587
Read1(QC-failed)	0	0
Read2	11318379	9895587
Read2(QC-failed)	0	0
Properly Paired	22636758	19791174
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	22636758	19791174
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	22186
Np	0
N optimal	22186
N conservative	22186
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.	115
Corr. Est. Fragment Len.	0.1986
Phantom Peak	50
Corr. Phantom Peak	0.2680
Argmin. Corr.	1500
Min. Corr.	0.1826
NSC	1.0876
RSC	0.1873

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	0.0239

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	0.2231
AUC	0.4914
CHANCE divergence	0.2215
Elbow Point	0.0000
JS Distance	0.6143
Synthetic AUC	0.5125
Synthetic Elbow Point	0.1299
Synthetic JS Distance	0.3065