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Report generated at 2020-05-26 16:30:48

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	144036734	142243746
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	142757684	139861369
Mapped(QC-failed)	0	0
% Mapped	99.1100	98.3300
Paired	144036734	142243746
Paired(QC-failed)	0	0
Read1	72018367	71121873
Read1(QC-failed)	0	0
Read2	72018367	71121873
Read2(QC-failed)	0	0
Properly Paired	141193468	135806036
Properly Paired(QC-failed)	0	0
% Properly Paired	98.0300	95.4700
With itself	141925892	138838091
With itself(QC-failed)	0	0
Singletons	831792	1023278
Singletons(QC-failed)	0	0
% Singleton	0.5800	0.7200
Diff. Chroms	188781	157069
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	65662044	59531888
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1505710	506734
Paired Opt. Dupes	2151	2429
% Dupes/100	0.0229	0.0085

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	65657350	59519061
Distinct Read Pairs	64151871	59013494
One Read Pair	62683017	58531991
Two Read Pairs	1433927	471637
NRF = Distinct/Total	0.9771	0.9915
PBC1 = OnePair/Distinct	0.9771	0.9918
PBC2 = OnePair/TwoPair	43.7142	124.1039

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	128312668	118050308
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	128312668	118050308
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	128312668	118050308
Paired(QC-failed)	0	0
Read1	64156334	59025154
Read1(QC-failed)	0	0
Read2	64156334	59025154
Read2(QC-failed)	0	0
Properly Paired	128312668	118050308
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	128312668	118050308
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	267393
Np	0
N optimal	267393
N conservative	267393
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.	145
Corr. Est. Fragment Len.	0.1764
Phantom Peak	45
Corr. Phantom Peak	0.1743
Argmin. Corr.	1500
Min. Corr.	0.1703
NSC	1.0356
RSC	1.5286

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	0.3048

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	0.2380
AUC	0.4964
CHANCE divergence	0.1031
Elbow Point	0.0000
JS Distance	0.6712
Synthetic AUC	0.5058
Synthetic Elbow Point	0.2020
Synthetic JS Distance	0.3496