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Report generated at 2020-05-10 12:55:26

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	56928844	94394890
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53534703	90679650
Mapped(QC-failed)	0	0
% Mapped	94.0400	96.0600
Paired	56928844	94394890
Paired(QC-failed)	0	0
Read1	28464422	47197445
Read1(QC-failed)	0	0
Read2	28464422	47197445
Read2(QC-failed)	0	0
Properly Paired	52210729	85747226
Properly Paired(QC-failed)	0	0
% Properly Paired	91.7100	90.8400
With itself	52857869	88391054
With itself(QC-failed)	0	0
Singletons	676834	2288596
Singletons(QC-failed)	0	0
% Singleton	1.1900	2.4200
Diff. Chroms	338151	1671322
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	22318425	36214131
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	134369	344208
Paired Opt. Dupes	1448	1746
% Dupes/100	0.0060	0.0095

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	22317707	36209957
Distinct Read Pairs	22183344	35865787
One Read Pair	22049730	35524443
Two Read Pairs	132871	338545
NRF = Distinct/Total	0.9940	0.9905
PBC1 = OnePair/Distinct	0.9940	0.9905
PBC2 = OnePair/TwoPair	165.9484	104.9327

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	44368112	71739846
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	44368112	71739846
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	44368112	71739846
Paired(QC-failed)	0	0
Read1	22184056	35869923
Read1(QC-failed)	0	0
Read2	22184056	35869923
Read2(QC-failed)	0	0
Properly Paired	44368112	71739846
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	44368112	71739846
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	46225
Np	0
N optimal	46225
N conservative	46225
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.	235
Corr. Est. Fragment Len.	0.1864
Phantom Peak	50
Corr. Phantom Peak	0.1964
Argmin. Corr.	1500
Min. Corr.	0.1766
NSC	1.0555
RSC	0.4949

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	0.0518

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	0.2075
AUC	0.4939
CHANCE divergence	0.2350
Elbow Point	0.0000
JS Distance	0.6270
Synthetic AUC	0.5036
Synthetic Elbow Point	0.0758
Synthetic JS Distance	0.3389