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Report generated at 2019-10-13 08:38:30

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	129829936	90571450
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	126966457	89141373
Mapped(QC-failed)	0	0
% Mapped	97.7900	98.4200
Paired	129829936	90571450
Paired(QC-failed)	0	0
Read1	64914968	45285725
Read1(QC-failed)	0	0
Read2	64914968	45285725
Read2(QC-failed)	0	0
Properly Paired	124979268	88372908
Properly Paired(QC-failed)	0	0
% Properly Paired	96.2600	97.5700
With itself	125246179	88783529
With itself(QC-failed)	0	0
Singletons	1720278	357844
Singletons(QC-failed)	0	0
% Singleton	1.3300	0.4000
Diff. Chroms	80409	165137
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	56548476	39015967
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	20348148	627860
Paired Opt. Dupes	3465	3635
% Dupes/100	0.3598	0.0161

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	56544333	38965090
Distinct Read Pairs	36197669	38338878
One Read Pair	23650082	37724707
Two Read Pairs	7673741	603360
NRF = Distinct/Total	0.6402	0.9839
PBC1 = OnePair/Distinct	0.6534	0.9840
PBC2 = OnePair/TwoPair	3.0819	62.5244

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	72400656	76776214
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	72400656	76776214
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	72400656	76776214
Paired(QC-failed)	0	0
Read1	36200328	38388107
Read1(QC-failed)	0	0
Read2	36200328	38388107
Read2(QC-failed)	0	0
Properly Paired	72400656	76776214
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	72400656	76776214
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	162547
Np	0
N optimal	162547
N conservative	162547
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.	230
Corr. Est. Fragment Len.	0.1675
Phantom Peak	50
Corr. Phantom Peak	0.1684
Argmin. Corr.	1500
Min. Corr.	0.1564
NSC	1.0708
RSC	0.9210

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	0.4267

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	0.1886
AUC	0.4952
CHANCE divergence	0.1313
Elbow Point	0.0000
JS Distance	0.7501
Synthetic AUC	0.4995
Synthetic Elbow Point	0.2886
Synthetic JS Distance	0.4259