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Report generated at 2020-07-01 17:39:36

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	251163732	172537646
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	247459367	169623973
Mapped(QC-failed)	0	0
% Mapped	98.5300	98.3100
Paired	251163732	172537646
Paired(QC-failed)	0	0
Read1	125581866	86268823
Read1(QC-failed)	0	0
Read2	125581866	86268823
Read2(QC-failed)	0	0
Properly Paired	243920151	167189057
Properly Paired(QC-failed)	0	0
% Properly Paired	97.1200	96.9000
With itself	245506555	168209600
With itself(QC-failed)	0	0
Singletons	1952812	1414373
Singletons(QC-failed)	0	0
% Singleton	0.7800	0.8200
Diff. Chroms	243161	219989
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	111025515	73240552
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7921559	4951054
Paired Opt. Dupes	4216	3082
% Dupes/100	0.0713	0.0676

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	111019903	73151406
Distinct Read Pairs	103098711	68207381
One Read Pair	95704080	63530327
Two Read Pairs	6902536	4425954
NRF = Distinct/Total	0.9287	0.9324
PBC1 = OnePair/Distinct	0.9283	0.9314
PBC2 = OnePair/TwoPair	13.8651	14.3540

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	206207912	136578996
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	206207912	136578996
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	206207912	136578996
Paired(QC-failed)	0	0
Read1	103103956	68289498
Read1(QC-failed)	0	0
Read2	103103956	68289498
Read2(QC-failed)	0	0
Properly Paired	206207912	136578996
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	206207912	136578996
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	199518
Np	0
N optimal	199518
N conservative	199518
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.	0.1928
Phantom Peak	50
Corr. Phantom Peak	0.1964
Argmin. Corr.	1500
Min. Corr.	0.1811
NSC	1.0644
RSC	0.7642

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	0.5770

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	0.1697
AUC	0.4972
CHANCE divergence	0.0966
Elbow Point	0.0000
JS Distance	0.7898
Synthetic AUC	0.4976
Synthetic Elbow Point	0.3833
Synthetic JS Distance	0.4808