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Report generated at 2020-05-14 16:45:03

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	121273294	153209202
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	116677388	149479073
Mapped(QC-failed)	0	0
% Mapped	96.2100	97.5700
Paired	121273294	153209202
Paired(QC-failed)	0	0
Read1	60636647	76604601
Read1(QC-failed)	0	0
Read2	60636647	76604601
Read2(QC-failed)	0	0
Properly Paired	115293313	147025179
Properly Paired(QC-failed)	0	0
% Properly Paired	95.0700	95.9600
With itself	116206912	148752327
With itself(QC-failed)	0	0
Singletons	470476	726746
Singletons(QC-failed)	0	0
% Singleton	0.3900	0.4700
Diff. Chroms	566250	985943
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	52847249	64024172
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	226015	238168
Paired Opt. Dupes	1313	1074
% Dupes/100	0.0043	0.0037

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	52842189	63953335
Distinct Read Pairs	52616194	63716435
One Read Pair	52391149	63481990
Two Read Pairs	224104	232337
NRF = Distinct/Total	0.9957	0.9963
PBC1 = OnePair/Distinct	0.9957	0.9963
PBC2 = OnePair/TwoPair	233.7805	273.2324

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	105242468	127572008
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	105242468	127572008
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	105242468	127572008
Paired(QC-failed)	0	0
Read1	52621234	63786004
Read1(QC-failed)	0	0
Read2	52621234	63786004
Read2(QC-failed)	0	0
Properly Paired	105242468	127572008
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	105242468	127572008
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	232059
Np	0
N optimal	232059
N conservative	232059
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.	140
Corr. Est. Fragment Len.	0.1861
Phantom Peak	50
Corr. Phantom Peak	0.1907
Argmin. Corr.	1500
Min. Corr.	0.1771
NSC	1.0509
RSC	0.6610

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	0.3448

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	0.2155
AUC	0.4960
CHANCE divergence	0.1120
Elbow Point	0.0000
JS Distance	0.7015
Synthetic AUC	0.5027
Synthetic Elbow Point	0.2338
Synthetic JS Distance	0.3861