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Report generated at 2020-05-03 17:50:18

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	120451752	136790320
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	116806513	132380851
Mapped(QC-failed)	0	0
% Mapped	96.9700	96.7800
Paired	120451752	136790320
Paired(QC-failed)	0	0
Read1	60225876	68395160
Read1(QC-failed)	0	0
Read2	60225876	68395160
Read2(QC-failed)	0	0
Properly Paired	115537533	130092484
Properly Paired(QC-failed)	0	0
% Properly Paired	95.9200	95.1000
With itself	116286949	131677058
With itself(QC-failed)	0	0
Singletons	519564	703793
Singletons(QC-failed)	0	0
% Singleton	0.4300	0.5100
Diff. Chroms	328281	604160
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	50383063	56350303
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	319154	241110
Paired Opt. Dupes	1878	2032
% Dupes/100	0.0063	0.0043

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	50377878	56321306
Distinct Read Pairs	50058759	56080639
One Read Pair	49741605	55842177
Two Read Pairs	315220	236573
NRF = Distinct/Total	0.9937	0.9957
PBC1 = OnePair/Distinct	0.9937	0.9957
PBC2 = OnePair/TwoPair	157.7996	236.0463

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	100127818	112218386
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	100127818	112218386
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	100127818	112218386
Paired(QC-failed)	0	0
Read1	50063909	56109193
Read1(QC-failed)	0	0
Read2	50063909	56109193
Read2(QC-failed)	0	0
Properly Paired	100127818	112218386
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	100127818	112218386
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	226405
Np	0
N optimal	226405
N conservative	226405
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.	125
Corr. Est. Fragment Len.	0.2321
Phantom Peak	50
Corr. Phantom Peak	0.2423
Argmin. Corr.	1500
Min. Corr.	0.2206
NSC	1.0523
RSC	0.5327

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	0.1760

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	0.2283
AUC	0.4959
CHANCE divergence	0.1232
Elbow Point	0.0000
JS Distance	0.6446
Synthetic AUC	0.4980
Synthetic Elbow Point	0.1074
Synthetic JS Distance	0.3596