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Report generated at 2019-10-13 01:24:20

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	93575092	90571450
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	86964999	89141373
Mapped(QC-failed)	0	0
% Mapped	92.9400	98.4200
Paired	93575092	90571450
Paired(QC-failed)	0	0
Read1	46787546	45285725
Read1(QC-failed)	0	0
Read2	46787546	45285725
Read2(QC-failed)	0	0
Properly Paired	86330133	88372908
Properly Paired(QC-failed)	0	0
% Properly Paired	92.2600	97.5700
With itself	86619626	88783529
With itself(QC-failed)	0	0
Singletons	345373	357844
Singletons(QC-failed)	0	0
% Singleton	0.3700	0.4000
Diff. Chroms	57035	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	39582099	39015967
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1121119	627860
Paired Opt. Dupes	3396	3635
% Dupes/100	0.0283	0.0161

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	39577146	38965090
Distinct Read Pairs	38456155	38338878
One Read Pair	37364649	37724707
Two Read Pairs	1062772	603360
NRF = Distinct/Total	0.9717	0.9839
PBC1 = OnePair/Distinct	0.9716	0.9840
PBC2 = OnePair/TwoPair	35.1577	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	76921960	76776214
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	76921960	76776214
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	76921960	76776214
Paired(QC-failed)	0	0
Read1	38460980	38388107
Read1(QC-failed)	0	0
Read2	38460980	38388107
Read2(QC-failed)	0	0
Properly Paired	76921960	76776214
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	76921960	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	59032
Np	0
N optimal	59032
N conservative	59032
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.	185
Corr. Est. Fragment Len.	0.3767
Phantom Peak	55
Corr. Phantom Peak	0.3345
Argmin. Corr.	1500
Min. Corr.	0.1922
NSC	1.9598
RSC	1.2963

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	0.5606

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	0.1279
AUC	0.4953
CHANCE divergence	0.1401
Elbow Point	0.0000
JS Distance	0.8914
Synthetic AUC	0.4975
Synthetic Elbow Point	0.5047
Synthetic JS Distance	0.5814