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Report generated at 2019-11-03 18:44:25

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	131098748	144885712
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	125802110	141771472
Mapped(QC-failed)	0	0
% Mapped	95.9600	97.8500
Paired	131098748	144885712
Paired(QC-failed)	0	0
Read1	65549374	72442856
Read1(QC-failed)	0	0
Read2	65549374	72442856
Read2(QC-failed)	0	0
Properly Paired	122716328	139161591
Properly Paired(QC-failed)	0	0
% Properly Paired	93.6100	96.0500
With itself	124391677	140839614
With itself(QC-failed)	0	0
Singletons	1410433	931858
Singletons(QC-failed)	0	0
% Singleton	1.0800	0.6400
Diff. Chroms	400621	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	45845402	61727393
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1845581	1553623
Paired Opt. Dupes	11337	14884
% Dupes/100	0.0403	0.0252

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	45844394	61648150
Distinct Read Pairs	43998850	60097677
One Read Pair	42218053	58572284
Two Read Pairs	1720409	1501098
NRF = Distinct/Total	0.9597	0.9748
PBC1 = OnePair/Distinct	0.9595	0.9746
PBC2 = OnePair/TwoPair	24.5395	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	87999642	120347540
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	87999642	120347540
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	87999642	120347540
Paired(QC-failed)	0	0
Read1	43999821	60173770
Read1(QC-failed)	0	0
Read2	43999821	60173770
Read2(QC-failed)	0	0
Properly Paired	87999642	120347540
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	87999642	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	214326
Np	0
N optimal	214326
N conservative	214326
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.	110
Corr. Est. Fragment Len.	0.2048
Phantom Peak	50
Corr. Phantom Peak	0.2442
Argmin. Corr.	1500
Min. Corr.	0.1946
NSC	1.0525
RSC	0.2060

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	0.2719

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	0.2111
AUC	0.4957
CHANCE divergence	0.1254
Elbow Point	0.0000
JS Distance	0.6679
Synthetic AUC	0.5014
Synthetic Elbow Point	0.2589
Synthetic JS Distance	0.3884