Untitled

No description

Report generated at 2020-05-02 07:12:40

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	40548444	53978528
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	37218837	49170795
Mapped(QC-failed)	0	0
% Mapped	91.7900	91.0900
Paired	40548444	53978528
Paired(QC-failed)	0	0
Read1	20274222	26989264
Read1(QC-failed)	0	0
Read2	20274222	26989264
Read2(QC-failed)	0	0
Properly Paired	35943459	47390286
Properly Paired(QC-failed)	0	0
% Properly Paired	88.6400	87.7900
With itself	36602280	48351213
With itself(QC-failed)	0	0
Singletons	616557	819582
Singletons(QC-failed)	0	0
% Singleton	1.5200	1.5200
Diff. Chroms	470360	552046
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	16390718	19555064
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	293010	746123
Paired Opt. Dupes	3202	2623
% Dupes/100	0.0179	0.0382

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	16390316	19555000
Distinct Read Pairs	16097318	18808880
One Read Pair	15808704	18086571
Two Read Pairs	284274	699153
NRF = Distinct/Total	0.9821	0.9618
PBC1 = OnePair/Distinct	0.9821	0.9616
PBC2 = OnePair/TwoPair	55.6108	25.8693

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	32195416	37617882
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	32195416	37617882
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	32195416	37617882
Paired(QC-failed)	0	0
Read1	16097708	18808941
Read1(QC-failed)	0	0
Read2	16097708	18808941
Read2(QC-failed)	0	0
Properly Paired	32195416	37617882
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	32195416	37617882
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	31340
Np	0
N optimal	31340
N conservative	31340
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.	255
Corr. Est. Fragment Len.	0.4304
Phantom Peak	55
Corr. Phantom Peak	0.3553
Argmin. Corr.	1500
Min. Corr.	0.1753
NSC	2.4546
RSC	1.4169

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	0.5376

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	0.0681
AUC	0.4927
CHANCE divergence	0.5154
Elbow Point	0.0000
JS Distance	0.8094
Synthetic AUC	0.5042
Synthetic Elbow Point	0.4241
Synthetic JS Distance	0.5844