Untitled

No description

Report generated at 2020-05-20 21:57:48

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	105722550	172040776
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	58614772	166313177
Mapped(QC-failed)	0	0
% Mapped	55.4400	96.6700
Paired	105722550	172040776
Paired(QC-failed)	0	0
Read1	52861275	86020388
Read1(QC-failed)	0	0
Read2	52861275	86020388
Read2(QC-failed)	0	0
Properly Paired	57481460	164316966
Properly Paired(QC-failed)	0	0
% Properly Paired	54.3700	95.5100
With itself	57755176	165368990
With itself(QC-failed)	0	0
Singletons	859596	944187
Singletons(QC-failed)	0	0
% Singleton	0.8100	0.5500
Diff. Chroms	86953	377471
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	24951699	70615481
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	243253	448995
Paired Opt. Dupes	685	1973
% Dupes/100	0.0097	0.0064

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	24944738	70604488
Distinct Read Pairs	24701566	70155597
One Read Pair	24460765	69710274
Two Read Pairs	238465	441873
NRF = Distinct/Total	0.9903	0.9936
PBC1 = OnePair/Distinct	0.9903	0.9937
PBC2 = OnePair/TwoPair	102.5759	157.7609

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	49416892	140332972
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	49416892	140332972
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	49416892	140332972
Paired(QC-failed)	0	0
Read1	24708446	70166486
Read1(QC-failed)	0	0
Read2	24708446	70166486
Read2(QC-failed)	0	0
Properly Paired	49416892	140332972
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	49416892	140332972
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	50331
Np	0
N optimal	50331
N conservative	50331
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.	110
Corr. Est. Fragment Len.	0.1774
Phantom Peak	50
Corr. Phantom Peak	0.2160
Argmin. Corr.	1500
Min. Corr.	0.1677
NSC	1.0580
RSC	0.2014

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	0.0594

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	0.2669
AUC	0.4942
CHANCE divergence	0.1267
Elbow Point	0.0000
JS Distance	0.5826
Synthetic AUC	0.5088
Synthetic Elbow Point	0.1002
Synthetic JS Distance	0.2880