Untitled

No description

Report generated at 2019-10-13 01:20:47

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	103558764	82773480
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	100744110	80507886
Mapped(QC-failed)	0	0
% Mapped	97.2800	97.2600
Paired	103558764	82773480
Paired(QC-failed)	0	0
Read1	51779382	41386740
Read1(QC-failed)	0	0
Read2	51779382	41386740
Read2(QC-failed)	0	0
Properly Paired	99700602	79812046
Properly Paired(QC-failed)	0	0
% Properly Paired	96.2700	96.4200
With itself	100168682	80154101
With itself(QC-failed)	0	0
Singletons	575428	353785
Singletons(QC-failed)	0	0
% Singleton	0.5600	0.4300
Diff. Chroms	111514	116542
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	42879559	35609282
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1918123	3238943
Paired Opt. Dupes	9993	8059
% Dupes/100	0.0447	0.0910

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42878250	35576205
Distinct Read Pairs	40960177	32340103
One Read Pair	39132536	29415039
Two Read Pairs	1749209	2647904
NRF = Distinct/Total	0.9553	0.9090
PBC1 = OnePair/Distinct	0.9554	0.9096
PBC2 = OnePair/TwoPair	22.3716	11.1088

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	81922872	64740678
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	81922872	64740678
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	81922872	64740678
Paired(QC-failed)	0	0
Read1	40961436	32370339
Read1(QC-failed)	0	0
Read2	40961436	32370339
Read2(QC-failed)	0	0
Properly Paired	81922872	64740678
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	81922872	64740678
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	23268
Np	0
N optimal	23268
N conservative	23268
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.	120
Corr. Est. Fragment Len.	0.1816
Phantom Peak	50
Corr. Phantom Peak	0.2035
Argmin. Corr.	1500
Min. Corr.	0.1755
NSC	1.0347
RSC	0.2181

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	0.0129

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	0.3068
AUC	0.4955
CHANCE divergence	0.1090
Elbow Point	0.0000
JS Distance	0.5285
Synthetic AUC	0.5047
Synthetic Elbow Point	0.0334
Synthetic JS Distance	0.2331