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Report generated at 2021-03-18 00:48:43

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	42904238	32633358
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	39949168	32017375
Mapped(QC-failed)	0	0
% Mapped	93.1100	98.1100
Paired	42904238	32633358
Paired(QC-failed)	0	0
Read1	21452119	16316679
Read1(QC-failed)	0	0
Read2	21452119	16316679
Read2(QC-failed)	0	0
Properly Paired	38696859	31194037
Properly Paired(QC-failed)	0	0
% Properly Paired	90.1900	95.5900
With itself	39621190	31710601
With itself(QC-failed)	0	0
Singletons	327978	306774
Singletons(QC-failed)	0	0
% Singleton	0.7600	0.9400
Diff. Chroms	179008	307689
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	17487551	13749916
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3225793	466098
Paired Opt. Dupes	1229	702
% Dupes/100	0.1845	0.0339

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	17482110	13728708
Distinct Read Pairs	14257425	13265289
One Read Pair	11520732	12815823
Two Read Pairs	2318718	436590
NRF = Distinct/Total	0.8155	0.9662
PBC1 = OnePair/Distinct	0.8081	0.9661
PBC2 = OnePair/TwoPair	4.9686	29.3544

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	28523516	26567636
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	28523516	26567636
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	28523516	26567636
Paired(QC-failed)	0	0
Read1	14261758	13283818
Read1(QC-failed)	0	0
Read2	14261758	13283818
Read2(QC-failed)	0	0
Properly Paired	28523516	26567636
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	28523516	26567636
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	51671
Np	0
N optimal	51671
N conservative	51671
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.	150
Corr. Est. Fragment Len.	0.1608
Phantom Peak	50
Corr. Phantom Peak	0.1519
Argmin. Corr.	1500
Min. Corr.	0.1430
NSC	1.1251
RSC	1.9919

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	0.0773

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	0.2585
AUC	0.4924
CHANCE divergence	0.1614
Elbow Point	0.0000
JS Distance	0.5835
Synthetic AUC	0.4993
Synthetic Elbow Point	0.0831
Synthetic JS Distance	0.2837