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Report generated at 2019-11-03 22:23:29

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	215262356	144885712
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	212683804	141771472
Mapped(QC-failed)	0	0
% Mapped	98.8000	97.8500
Paired	215262356	144885712
Paired(QC-failed)	0	0
Read1	107631178	72442856
Read1(QC-failed)	0	0
Read2	107631178	72442856
Read2(QC-failed)	0	0
Properly Paired	210042281	139161591
Properly Paired(QC-failed)	0	0
% Properly Paired	97.5800	96.0500
With itself	211693930	140839614
With itself(QC-failed)	0	0
Singletons	989874	931858
Singletons(QC-failed)	0	0
% Singleton	0.4600	0.6400
Diff. Chroms	691575	862243
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	93696029	61727393
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3401573	1553623
Paired Opt. Dupes	21344	14884
% Dupes/100	0.0363	0.0252

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	93693303	61648150
Distinct Read Pairs	90291823	60097677
One Read Pair	86985704	58572284
Two Read Pairs	3213370	1501098
NRF = Distinct/Total	0.9637	0.9748
PBC1 = OnePair/Distinct	0.9634	0.9746
PBC2 = OnePair/TwoPair	27.0699	39.0196

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	180588912	120347540
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	180588912	120347540
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	180588912	120347540
Paired(QC-failed)	0	0
Read1	90294456	60173770
Read1(QC-failed)	0	0
Read2	90294456	60173770
Read2(QC-failed)	0	0
Properly Paired	180588912	120347540
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	180588912	120347540
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	41417
Np	0
N optimal	41417
N conservative	41417
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.	125
Corr. Est. Fragment Len.	0.1709
Phantom Peak	50
Corr. Phantom Peak	0.1762
Argmin. Corr.	1500
Min. Corr.	0.1692
NSC	1.0104
RSC	0.2490

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	0.0137

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	0.3450
AUC	0.4970
CHANCE divergence	0.0918
Elbow Point	0.0000
JS Distance	0.4805
Synthetic AUC	0.5025
Synthetic Elbow Point	0.0325
Synthetic JS Distance	0.1852