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Report generated at 2020-06-05 17:26:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	92436146	50431816
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	91277959	48831892
Mapped(QC-failed)	0	0
% Mapped	98.7500	96.8300
Paired	92436146	50431816
Paired(QC-failed)	0	0
Read1	46218073	25215908
Read1(QC-failed)	0	0
Read2	46218073	25215908
Read2(QC-failed)	0	0
Properly Paired	90453564	47916697
Properly Paired(QC-failed)	0	0
% Properly Paired	97.8600	95.0100
With itself	90844663	48429061
With itself(QC-failed)	0	0
Singletons	433296	402831
Singletons(QC-failed)	0	0
% Singleton	0.4700	0.8000
Diff. Chroms	139028	115649
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	40372319	21176027
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	526213	1364540
Paired Opt. Dupes	17285	7918
% Dupes/100	0.0130	0.0644

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	40371154	21155539
Distinct Read Pairs	39844963	19792555
One Read Pair	39324844	18512617
Two Read Pairs	514175	1202837
NRF = Distinct/Total	0.9870	0.9356
PBC1 = OnePair/Distinct	0.9869	0.9353
PBC2 = OnePair/TwoPair	76.4814	15.3908

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	79692212	39622974
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	79692212	39622974
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	79692212	39622974
Paired(QC-failed)	0	0
Read1	39846106	19811487
Read1(QC-failed)	0	0
Read2	39846106	19811487
Read2(QC-failed)	0	0
Properly Paired	79692212	39622974
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	79692212	39622974
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	192548
Np	0
N optimal	192548
N conservative	192548
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.	0.1833
Phantom Peak	50
Corr. Phantom Peak	0.1902
Argmin. Corr.	1500
Min. Corr.	0.1796
NSC	1.0207
RSC	0.3493

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	0.2761

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	0.2004
AUC	0.4954
CHANCE divergence	0.1235
Elbow Point	0.0000
JS Distance	0.7263
Synthetic AUC	0.5078
Synthetic Elbow Point	0.2208
Synthetic JS Distance	0.4055