Untitled

No description

Report generated at 2019-12-03 11:38:54

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	74188332	96981564
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	68470149	94057636
Mapped(QC-failed)	0	0
% Mapped	92.2900	96.9900
Paired	74188332	96981564
Paired(QC-failed)	0	0
Read1	37094166	48490782
Read1(QC-failed)	0	0
Read2	37094166	48490782
Read2(QC-failed)	0	0
Properly Paired	68069668	90998199
Properly Paired(QC-failed)	0	0
% Properly Paired	91.7500	93.8300
With itself	68261947	93287611
With itself(QC-failed)	0	0
Singletons	208202	770025
Singletons(QC-failed)	0	0
% Singleton	0.2800	0.7900
Diff. Chroms	41440	205681
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	32005566	40192164
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1879421	554748
Paired Opt. Dupes	1969	11605
% Dupes/100	0.0587	0.0138

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	32005261	40177379
Distinct Read Pairs	30125865	39622917
One Read Pair	28351468	39079490
Two Read Pairs	1674724	534171
NRF = Distinct/Total	0.9413	0.9862
PBC1 = OnePair/Distinct	0.9411	0.9863
PBC2 = OnePair/TwoPair	16.9290	73.1591

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	60252290	79274832
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	60252290	79274832
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	60252290	79274832
Paired(QC-failed)	0	0
Read1	30126145	39637416
Read1(QC-failed)	0	0
Read2	30126145	39637416
Read2(QC-failed)	0	0
Properly Paired	60252290	79274832
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	60252290	79274832
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	88385
Np	0
N optimal	88385
N conservative	88385
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.	160
Corr. Est. Fragment Len.	0.4054
Phantom Peak	55
Corr. Phantom Peak	0.3621
Argmin. Corr.	1500
Min. Corr.	0.2241
NSC	1.8090
RSC	1.3141

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	0.6736

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	0.0670
AUC	0.4947
CHANCE divergence	0.3664
Elbow Point	0.0000
JS Distance	0.8629
Synthetic AUC	0.5018
Synthetic Elbow Point	0.5492
Synthetic JS Distance	0.6385