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Report generated at 2022-01-13 16:30:22

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	75594748	61483794
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	70510568	53537979
Mapped(QC-failed)	0	0
% Mapped	93.2700	87.0800
Paired	75594748	61483794
Paired(QC-failed)	0	0
Read1	37797374	30741897
Read1(QC-failed)	0	0
Read2	37797374	30741897
Read2(QC-failed)	0	0
Properly Paired	68355177	45512545
Properly Paired(QC-failed)	0	0
% Properly Paired	90.4200	74.0200
With itself	69072936	48321091
With itself(QC-failed)	0	0
Singletons	1437632	5216888
Singletons(QC-failed)	0	0
% Singleton	1.9000	8.4800
Diff. Chroms	490461	1709831
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	30654634	7051123
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1054354	302597
Paired Opt. Dupes	5188	868
% Dupes/100	0.0344	0.0429

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	30653965	7050084
Distinct Read Pairs	29599635	6747724
One Read Pair	28577535	6457557
Two Read Pairs	990713	279052
NRF = Distinct/Total	0.9656	0.9571
PBC1 = OnePair/Distinct	0.9655	0.9570
PBC2 = OnePair/TwoPair	28.8454	23.1411

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	59200560	13497052
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	59200560	13497052
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	59200560	13497052
Paired(QC-failed)	0	0
Read1	29600280	6748526
Read1(QC-failed)	0	0
Read2	29600280	6748526
Read2(QC-failed)	0	0
Properly Paired	59200560	13497052
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	59200560	13497052
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	77979
Np	0
N optimal	77979
N conservative	77979
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.	0.1820
Phantom Peak	50
Corr. Phantom Peak	0.1850
Argmin. Corr.	1500
Min. Corr.	0.1741
NSC	1.0453
RSC	0.7221

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	0.1338

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	0.2136
AUC	0.4947
CHANCE divergence	0.1329
Elbow Point	0.0000
JS Distance	0.6994
Synthetic AUC	0.4974
Synthetic Elbow Point	0.0836
Synthetic JS Distance	0.3776