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Report generated at 2020-05-19 03:49:13

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	149648828	173400002
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	139548626	168920220
Mapped(QC-failed)	0	0
% Mapped	93.2500	97.4200
Paired	149648828	173400002
Paired(QC-failed)	0	0
Read1	74824414	86700001
Read1(QC-failed)	0	0
Read2	74824414	86700001
Read2(QC-failed)	0	0
Properly Paired	137586664	165589734
Properly Paired(QC-failed)	0	0
% Properly Paired	91.9400	95.5000
With itself	138632349	168052672
With itself(QC-failed)	0	0
Singletons	916277	867548
Singletons(QC-failed)	0	0
% Singleton	0.6100	0.5000
Diff. Chroms	496254	1552539
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	60144500	72427157
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	457275	372440
Paired Opt. Dupes	1854	2435
% Dupes/100	0.0076	0.0051

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	60140666	72396327
Distinct Read Pairs	59683432	72024241
One Read Pair	59229957	71654541
Two Read Pairs	449756	367402
NRF = Distinct/Total	0.9924	0.9949
PBC1 = OnePair/Distinct	0.9924	0.9949
PBC2 = OnePair/TwoPair	131.6935	195.0304

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	119374450	144109434
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	119374450	144109434
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	119374450	144109434
Paired(QC-failed)	0	0
Read1	59687225	72054717
Read1(QC-failed)	0	0
Read2	59687225	72054717
Read2(QC-failed)	0	0
Properly Paired	119374450	144109434
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	119374450	144109434
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	207866
Np	0
N optimal	207866
N conservative	207866
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.	135
Corr. Est. Fragment Len.	0.1831
Phantom Peak	50
Corr. Phantom Peak	0.2033
Argmin. Corr.	1500
Min. Corr.	0.1743
NSC	1.0506
RSC	0.3047

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	0.1490

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	0.2571
AUC	0.4963
CHANCE divergence	0.1065
Elbow Point	0.0000
JS Distance	0.6098
Synthetic AUC	0.5011
Synthetic Elbow Point	0.1325
Synthetic JS Distance	0.3182