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Report generated at 2020-05-13 04:13:12

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	68831766	44822058
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	64540184	42270277
Mapped(QC-failed)	0	0
% Mapped	93.7700	94.3100
Paired	68831766	44822058
Paired(QC-failed)	0	0
Read1	34415883	22411029
Read1(QC-failed)	0	0
Read2	34415883	22411029
Read2(QC-failed)	0	0
Properly Paired	61092149	39106937
Properly Paired(QC-failed)	0	0
% Properly Paired	88.7600	87.2500
With itself	63297565	41498214
With itself(QC-failed)	0	0
Singletons	1242619	772063
Singletons(QC-failed)	0	0
% Singleton	1.8100	1.7200
Diff. Chroms	1489496	1698756
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	26531945	17000414
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	324428	184749
Paired Opt. Dupes	2482	1571
% Dupes/100	0.0122	0.0109

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	26531747	16997550
Distinct Read Pairs	26207319	16812850
One Read Pair	25886334	16629884
Two Read Pairs	317578	181248
NRF = Distinct/Total	0.9878	0.9891
PBC1 = OnePair/Distinct	0.9878	0.9891
PBC2 = OnePair/TwoPair	81.5117	91.7521

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	52415034	33631330
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	52415034	33631330
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	52415034	33631330
Paired(QC-failed)	0	0
Read1	26207517	16815665
Read1(QC-failed)	0	0
Read2	26207517	16815665
Read2(QC-failed)	0	0
Properly Paired	52415034	33631330
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	52415034	33631330
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	108390
Np	0
N optimal	108390
N conservative	108390
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.	270
Corr. Est. Fragment Len.	0.2018
Phantom Peak	50
Corr. Phantom Peak	0.1943
Argmin. Corr.	1500
Min. Corr.	0.1826
NSC	1.1055
RSC	1.6344

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	0.1984

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	0.1337
AUC	0.4943
CHANCE divergence	0.4184
Elbow Point	0.0000
JS Distance	0.6942
Synthetic AUC	0.4972
Synthetic Elbow Point	0.1094
Synthetic JS Distance	0.4080