Untitled

No description

Report generated at 2019-10-12 23:46:20

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	103706922	82773480
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	100537055	80507886
Mapped(QC-failed)	0	0
% Mapped	96.9400	97.2600
Paired	103706922	82773480
Paired(QC-failed)	0	0
Read1	51853461	41386740
Read1(QC-failed)	0	0
Read2	51853461	41386740
Read2(QC-failed)	0	0
Properly Paired	99861332	79812046
Properly Paired(QC-failed)	0	0
% Properly Paired	96.2900	96.4200
With itself	100156292	80154101
With itself(QC-failed)	0	0
Singletons	380763	353785
Singletons(QC-failed)	0	0
% Singleton	0.3700	0.4300
Diff. Chroms	103331	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	44920945	35609282
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2276697	3238943
Paired Opt. Dupes	10894	8059
% Dupes/100	0.0507	0.0910

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	44919762	35576205
Distinct Read Pairs	42643120	32340103
One Read Pair	40467332	29415039
Two Read Pairs	2079741	2647904
NRF = Distinct/Total	0.9493	0.9090
PBC1 = OnePair/Distinct	0.9490	0.9096
PBC2 = OnePair/TwoPair	19.4579	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	85288496	64740678
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	85288496	64740678
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	85288496	64740678
Paired(QC-failed)	0	0
Read1	42644248	32370339
Read1(QC-failed)	0	0
Read2	42644248	32370339
Read2(QC-failed)	0	0
Properly Paired	85288496	64740678
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	85288496	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	103173
Np	0
N optimal	103173
N conservative	103173
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.	205
Corr. Est. Fragment Len.	0.1733
Phantom Peak	50
Corr. Phantom Peak	0.1775
Argmin. Corr.	1500
Min. Corr.	0.1709
NSC	1.0141
RSC	0.3653

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	0.0912

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	0.2769
AUC	0.4956
CHANCE divergence	0.1126
Elbow Point	0.0000
JS Distance	0.5867
Synthetic AUC	0.4971
Synthetic Elbow Point	0.0510
Synthetic JS Distance	0.2787