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Report generated at 2021-10-21 19:02:47

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	149043542	249846494
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	146109542	245693039
Mapped(QC-failed)	0	0
% Mapped	98.0300	98.3400
Paired	149043542	249846494
Paired(QC-failed)	0	0
Read1	74521771	124923247
Read1(QC-failed)	0	0
Read2	74521771	124923247
Read2(QC-failed)	0	0
Properly Paired	142423806	234957962
Properly Paired(QC-failed)	0	0
% Properly Paired	95.5600	94.0400
With itself	145006029	243593650
With itself(QC-failed)	0	0
Singletons	1103513	2099389
Singletons(QC-failed)	0	0
% Singleton	0.7400	0.8400
Diff. Chroms	1981704	6531607
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	60564351	98092949
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4330008	7176563
Paired Opt. Dupes	54259	57044
% Dupes/100	0.0715	0.0732

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	60563378	98012771
Distinct Read Pairs	56233435	90842894
One Read Pair	52152740	84087873
Two Read Pairs	3844751	6363556
NRF = Distinct/Total	0.9285	0.9268
PBC1 = OnePair/Distinct	0.9274	0.9256
PBC2 = OnePair/TwoPair	13.5647	13.2140

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	112468686	181832772
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	112468686	181832772
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	112468686	181832772
Paired(QC-failed)	0	0
Read1	56234343	90916386
Read1(QC-failed)	0	0
Read2	56234343	90916386
Read2(QC-failed)	0	0
Properly Paired	112468686	181832772
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	112468686	181832772
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	117044
Np	0
N optimal	117044
N conservative	117044
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.	215
Corr. Est. Fragment Len.	0.2137
Phantom Peak	50
Corr. Phantom Peak	0.2141
Argmin. Corr.	1500
Min. Corr.	0.2056
NSC	1.0392
RSC	0.9527

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	0.7003

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	0.1048
AUC	0.4953
CHANCE divergence	0.1697
Elbow Point	0.0000
JS Distance	0.8283
Synthetic AUC	0.5055
Synthetic Elbow Point	0.5131
Synthetic JS Distance	0.5896