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Report generated at 2021-01-19 21:44:30

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	70130338	193594802
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	36203145	187969057
Mapped(QC-failed)	0	0
% Mapped	51.6200	97.0900
Paired	70130338	193594802
Paired(QC-failed)	0	0
Read1	35065169	96797401
Read1(QC-failed)	0	0
Read2	35065169	96797401
Read2(QC-failed)	0	0
Properly Paired	35487397	184287983
Properly Paired(QC-failed)	0	0
% Properly Paired	50.6000	95.1900
With itself	36027771	185784698
With itself(QC-failed)	0	0
Singletons	175374	2184359
Singletons(QC-failed)	0	0
% Singleton	0.2500	1.1300
Diff. Chroms	44975	610670
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	16243811	78211821
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	770440	539110
Paired Opt. Dupes	3627	19807
% Dupes/100	0.0474	0.0069

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	16199462	77646644
Distinct Read Pairs	15431896	77172156
One Read Pair	14698386	76701136
Two Read Pairs	700870	467668
NRF = Distinct/Total	0.9526	0.9939
PBC1 = OnePair/Distinct	0.9525	0.9939
PBC2 = OnePair/TwoPair	20.9716	164.0077

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	30946742	155345422
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	30946742	155345422
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	30946742	155345422
Paired(QC-failed)	0	0
Read1	15473371	77672711
Read1(QC-failed)	0	0
Read2	15473371	77672711
Read2(QC-failed)	0	0
Properly Paired	30946742	155345422
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	30946742	155345422
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	115290
Np	0
N optimal	115290
N conservative	115290
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.	0.1929
Phantom Peak	50
Corr. Phantom Peak	0.1915
Argmin. Corr.	1500
Min. Corr.	0.1703
NSC	1.1329
RSC	1.0682

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	0.2439

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	0.1981
AUC	0.4927
CHANCE divergence	0.2121
Elbow Point	0.0000
JS Distance	0.6750
Synthetic AUC	0.4950
Synthetic Elbow Point	0.2647
Synthetic JS Distance	0.3724