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Report generated at 2020-07-08 00:30:03

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	81068154	246240780
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	80383536	242844912
Mapped(QC-failed)	0	0
% Mapped	99.1600	98.6200
Paired	81068154	246240780
Paired(QC-failed)	0	0
Read1	40534077	123120390
Read1(QC-failed)	0	0
Read2	40534077	123120390
Read2(QC-failed)	0	0
Properly Paired	79954076	234365124
Properly Paired(QC-failed)	0	0
% Properly Paired	98.6300	95.1800
With itself	80083880	241490311
With itself(QC-failed)	0	0
Singletons	299656	1354601
Singletons(QC-failed)	0	0
% Singleton	0.3700	0.5500
Diff. Chroms	22335	217706
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	36650097	104468009
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1517691	1214525
Paired Opt. Dupes	2263	3857
% Dupes/100	0.0414	0.0116

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	36640370	104430837
Distinct Read Pairs	35123074	103222868
One Read Pair	33843347	102080686
Two Read Pairs	1127439	1115589
NRF = Distinct/Total	0.9586	0.9884
PBC1 = OnePair/Distinct	0.9636	0.9889
PBC2 = OnePair/TwoPair	30.0179	91.5038

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	70264812	206506968
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	70264812	206506968
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	70264812	206506968
Paired(QC-failed)	0	0
Read1	35132406	103253484
Read1(QC-failed)	0	0
Read2	35132406	103253484
Read2(QC-failed)	0	0
Properly Paired	70264812	206506968
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	70264812	206506968
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	62562
Np	0
N optimal	62562
N conservative	62562
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.	170
Corr. Est. Fragment Len.	0.2710
Phantom Peak	45
Corr. Phantom Peak	0.1951
Argmin. Corr.	1500
Min. Corr.	0.1622
NSC	1.6707
RSC	3.3091

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	0.5886

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	0.1271
AUC	0.4952
CHANCE divergence	0.1398
Elbow Point	0.0000
JS Distance	0.8984
Synthetic AUC	0.5083
Synthetic Elbow Point	0.5129
Synthetic JS Distance	0.5773