Untitled

No description

Report generated at 2020-05-03 11:03:32

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	93302704	137918120
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	91391690	134017182
Mapped(QC-failed)	0	0
% Mapped	97.9500	97.1700
Paired	93302704	137918120
Paired(QC-failed)	0	0
Read1	46651352	68959060
Read1(QC-failed)	0	0
Read2	46651352	68959060
Read2(QC-failed)	0	0
Properly Paired	90173843	131780584
Properly Paired(QC-failed)	0	0
% Properly Paired	96.6500	95.5500
With itself	91053554	133321503
With itself(QC-failed)	0	0
Singletons	338136	695679
Singletons(QC-failed)	0	0
% Singleton	0.3600	0.5000
Diff. Chroms	574702	866040
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	41107423	57429822
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	157618	221342
Paired Opt. Dupes	871	1051
% Dupes/100	0.0038	0.0039

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	41104894	57381583
Distinct Read Pairs	40947285	57160903
One Read Pair	40790260	56941874
Two Read Pairs	156449	217499
NRF = Distinct/Total	0.9962	0.9962
PBC1 = OnePair/Distinct	0.9962	0.9962
PBC2 = OnePair/TwoPair	260.7256	261.8029

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	81899610	114416960
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	81899610	114416960
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	81899610	114416960
Paired(QC-failed)	0	0
Read1	40949805	57208480
Read1(QC-failed)	0	0
Read2	40949805	57208480
Read2(QC-failed)	0	0
Properly Paired	81899610	114416960
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	81899610	114416960
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	119031
Np	0
N optimal	119031
N conservative	119031
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.	175
Corr. Est. Fragment Len.	0.1884
Phantom Peak	50
Corr. Phantom Peak	0.1928
Argmin. Corr.	1500
Min. Corr.	0.1778
NSC	1.0598
RSC	0.7058

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	0.2567

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	0.2321
AUC	0.4955
CHANCE divergence	0.1109
Elbow Point	0.0000
JS Distance	0.6867
Synthetic AUC	0.5002
Synthetic Elbow Point	0.2102
Synthetic JS Distance	0.3621