Untitled

No description

Report generated at 2020-07-14 09:07:14

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	50342840	100267900
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	49437019	98810234
Mapped(QC-failed)	0	0
% Mapped	98.2000	98.5500
Paired	50342840	100267900
Paired(QC-failed)	0	0
Read1	25171420	50133950
Read1(QC-failed)	0	0
Read2	25171420	50133950
Read2(QC-failed)	0	0
Properly Paired	49093438	95001356
Properly Paired(QC-failed)	0	0
% Properly Paired	97.5200	94.7500
With itself	49199548	98214055
With itself(QC-failed)	0	0
Singletons	237471	596179
Singletons(QC-failed)	0	0
% Singleton	0.4700	0.5900
Diff. Chroms	15108	104040
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	22861276	42286553
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3638578	313043
Paired Opt. Dupes	746	1742
% Dupes/100	0.1592	0.0074

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	22853513	42271771
Distinct Read Pairs	19216208	41959879
One Read Pair	16184018	41660125
Two Read Pairs	2585262	294758
NRF = Distinct/Total	0.8408	0.9926
PBC1 = OnePair/Distinct	0.8422	0.9929
PBC2 = OnePair/TwoPair	6.2601	141.3367

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	38445396	83947020
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	38445396	83947020
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	38445396	83947020
Paired(QC-failed)	0	0
Read1	19222698	41973510
Read1(QC-failed)	0	0
Read2	19222698	41973510
Read2(QC-failed)	0	0
Properly Paired	38445396	83947020
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	38445396	83947020
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	55886
Np	0
N optimal	55886
N conservative	55886
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.	0.3064
Phantom Peak	55
Corr. Phantom Peak	0.2099
Argmin. Corr.	1500
Min. Corr.	0.1706
NSC	1.7965
RSC	3.4561

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	0.5889

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	0.0949
AUC	0.4935
CHANCE divergence	0.2897
Elbow Point	0.0000
JS Distance	0.8743
Synthetic AUC	0.5020
Synthetic Elbow Point	0.5231
Synthetic JS Distance	0.5978