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Report generated at 2020-07-14 12:27:32

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	59288790	103857894
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	58815164	102353291
Mapped(QC-failed)	0	0
% Mapped	99.2000	98.5500
Paired	59288790	103857894
Paired(QC-failed)	0	0
Read1	29644395	51928947
Read1(QC-failed)	0	0
Read2	29644395	51928947
Read2(QC-failed)	0	0
Properly Paired	57680842	100340149
Properly Paired(QC-failed)	0	0
% Properly Paired	97.2900	96.6100
With itself	58522957	101801899
With itself(QC-failed)	0	0
Singletons	292207	551392
Singletons(QC-failed)	0	0
% Singleton	0.4900	0.5300
Diff. Chroms	29462	131984
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	26899935	44269160
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2794593	406091
Paired Opt. Dupes	351	1054
% Dupes/100	0.1039	0.0092

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	26898443	44267990
Distinct Read Pairs	24103869	43861911
One Read Pair	22295436	43470849
Two Read Pairs	1337587	382881
NRF = Distinct/Total	0.8961	0.9908
PBC1 = OnePair/Distinct	0.9250	0.9911
PBC2 = OnePair/TwoPair	16.6684	113.5362

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	48210684	87726138
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	48210684	87726138
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	48210684	87726138
Paired(QC-failed)	0	0
Read1	24105342	43863069
Read1(QC-failed)	0	0
Read2	24105342	43863069
Read2(QC-failed)	0	0
Properly Paired	48210684	87726138
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	48210684	87726138
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	68131
Np	0
N optimal	68131
N conservative	68131
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.	150
Corr. Est. Fragment Len.	0.3664
Phantom Peak	55
Corr. Phantom Peak	0.2094
Argmin. Corr.	1500
Min. Corr.	0.1276
NSC	2.8714
RSC	2.9177

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	0.7541

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	0.0549
AUC	0.4941
CHANCE divergence	0.3759
Elbow Point	0.0000
JS Distance	0.9280
Synthetic AUC	0.5101
Synthetic Elbow Point	0.6092
Synthetic JS Distance	0.6886