Untitled

No description

Report generated at 2019-10-13 04:35:10

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	123942856	70427534
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	120146001	69036340
Mapped(QC-failed)	0	0
% Mapped	96.9400	98.0200
Paired	123942856	70427534
Paired(QC-failed)	0	0
Read1	61971428	35213767
Read1(QC-failed)	0	0
Read2	61971428	35213767
Read2(QC-failed)	0	0
Properly Paired	119116405	68456801
Properly Paired(QC-failed)	0	0
% Properly Paired	96.1100	97.2000
With itself	119605806	68728853
With itself(QC-failed)	0	0
Singletons	540195	307487
Singletons(QC-failed)	0	0
% Singleton	0.4400	0.4400
Diff. Chroms	103667	67653
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	51024458	30027609
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	14075550	502205
Paired Opt. Dupes	9441	5522
% Dupes/100	0.2759	0.0167

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	51022460	29867632
Distinct Read Pairs	36947348	29376965
One Read Pair	26539486	28893133
Two Read Pairs	7637606	477131
NRF = Distinct/Total	0.7241	0.9836
PBC1 = OnePair/Distinct	0.7183	0.9835
PBC2 = OnePair/TwoPair	3.4748	60.5560

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	73897816	59050808
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	73897816	59050808
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	73897816	59050808
Paired(QC-failed)	0	0
Read1	36948908	29525404
Read1(QC-failed)	0	0
Read2	36948908	29525404
Read2(QC-failed)	0	0
Properly Paired	73897816	59050808
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	73897816	59050808
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	75301
Np	0
N optimal	75301
N conservative	75301
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.	150
Corr. Est. Fragment Len.	0.1709
Phantom Peak	50
Corr. Phantom Peak	0.1791
Argmin. Corr.	1500
Min. Corr.	0.1623
NSC	1.0530
RSC	0.5121

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	0.0391

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	0.2887
AUC	0.4953
CHANCE divergence	0.1242
Elbow Point	0.0000
JS Distance	0.5354
Synthetic AUC	0.4980
Synthetic Elbow Point	0.0793
Synthetic JS Distance	0.2561