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Report generated at 2020-05-20 20:59:15

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	119426994	177519184
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	105094911	172494915
Mapped(QC-failed)	0	0
% Mapped	88.0000	97.1700
Paired	119426994	177519184
Paired(QC-failed)	0	0
Read1	59713497	88759592
Read1(QC-failed)	0	0
Read2	59713497	88759592
Read2(QC-failed)	0	0
Properly Paired	103890516	168093297
Properly Paired(QC-failed)	0	0
% Properly Paired	86.9900	94.6900
With itself	104453403	170816950
With itself(QC-failed)	0	0
Singletons	641508	1677965
Singletons(QC-failed)	0	0
% Singleton	0.5400	0.9500
Diff. Chroms	272930	1509587
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	47905555	73622728
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	278010	559519
Paired Opt. Dupes	1830	3080
% Dupes/100	0.0058	0.0076

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	47903160	73528740
Distinct Read Pairs	47625166	72972791
One Read Pair	47348575	72421080
Two Read Pairs	275204	547586
NRF = Distinct/Total	0.9942	0.9924
PBC1 = OnePair/Distinct	0.9942	0.9924
PBC2 = OnePair/TwoPair	172.0490	132.2552

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	95255090	146126418
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	95255090	146126418
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	95255090	146126418
Paired(QC-failed)	0	0
Read1	47627545	73063209
Read1(QC-failed)	0	0
Read2	47627545	73063209
Read2(QC-failed)	0	0
Properly Paired	95255090	146126418
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	95255090	146126418
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	268152
Np	0
N optimal	268152
N conservative	268152
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.	0.1992
Phantom Peak	50
Corr. Phantom Peak	0.2060
Argmin. Corr.	1500
Min. Corr.	0.1786
NSC	1.1151
RSC	0.7516

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	0.3928

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	0.1593
AUC	0.4958
CHANCE divergence	0.2045
Elbow Point	0.0000
JS Distance	0.7235
Synthetic AUC	0.4981
Synthetic Elbow Point	0.2179
Synthetic JS Distance	0.4562