Untitled

No description

Report generated at 2020-05-22 21:38:46

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	75385646	192176210
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	74732084	189111270
Mapped(QC-failed)	0	0
% Mapped	99.1300	98.4100
Paired	75385646	192176210
Paired(QC-failed)	0	0
Read1	37692823	96088105
Read1(QC-failed)	0	0
Read2	37692823	96088105
Read2(QC-failed)	0	0
Properly Paired	74377798	185500997
Properly Paired(QC-failed)	0	0
% Properly Paired	98.6600	96.5300
With itself	74494176	188039219
With itself(QC-failed)	0	0
Singletons	237908	1072051
Singletons(QC-failed)	0	0
% Singleton	0.3200	0.5600
Diff. Chroms	20164	189715
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	34208042	81981512
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2689986	827169
Paired Opt. Dupes	1876	5791
% Dupes/100	0.0786	0.0101

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34196487	81951811
Distinct Read Pairs	31507239	81129436
One Read Pair	29454378	80347882
Two Read Pairs	1692053	763850
NRF = Distinct/Total	0.9214	0.9900
PBC1 = OnePair/Distinct	0.9348	0.9904
PBC2 = OnePair/TwoPair	17.4075	105.1880

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	63036112	162308686
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	63036112	162308686
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	63036112	162308686
Paired(QC-failed)	0	0
Read1	31518056	81154343
Read1(QC-failed)	0	0
Read2	31518056	81154343
Read2(QC-failed)	0	0
Properly Paired	63036112	162308686
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	63036112	162308686
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	66241
Np	0
N optimal	66241
N conservative	66241
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.	170
Corr. Est. Fragment Len.	0.3228
Phantom Peak	45
Corr. Phantom Peak	0.2080
Argmin. Corr.	1500
Min. Corr.	0.1377
NSC	2.3448
RSC	2.6333

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	0.6224

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	0.1040
AUC	0.4949
CHANCE divergence	0.1911
Elbow Point	0.0000
JS Distance	0.9026
Synthetic AUC	0.4964
Synthetic Elbow Point	0.5348
Synthetic JS Distance	0.6123