Untitled

No description

Report generated at 2019-11-03 15:36:12

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	137651722	144885712
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	133942426	141771472
Mapped(QC-failed)	0	0
% Mapped	97.3100	97.8500
Paired	137651722	144885712
Paired(QC-failed)	0	0
Read1	68825861	72442856
Read1(QC-failed)	0	0
Read2	68825861	72442856
Read2(QC-failed)	0	0
Properly Paired	131701270	139161591
Properly Paired(QC-failed)	0	0
% Properly Paired	95.6800	96.0500
With itself	133176373	140839614
With itself(QC-failed)	0	0
Singletons	766053	931858
Singletons(QC-failed)	0	0
% Singleton	0.5600	0.6400
Diff. Chroms	383437	862243
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	58864518	61727393
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	8920244	1553623
Paired Opt. Dupes	9690	14884
% Dupes/100	0.1515	0.0252

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	58853945	61648150
Distinct Read Pairs	49935259	60097677
One Read Pair	42150073	58572284
Two Read Pairs	6774122	1501098
NRF = Distinct/Total	0.8485	0.9748
PBC1 = OnePair/Distinct	0.8441	0.9746
PBC2 = OnePair/TwoPair	6.2222	39.0196

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	99888548	120347540
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	99888548	120347540
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	99888548	120347540
Paired(QC-failed)	0	0
Read1	49944274	60173770
Read1(QC-failed)	0	0
Read2	49944274	60173770
Read2(QC-failed)	0	0
Properly Paired	99888548	120347540
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	99888548	120347540
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	25476
Np	0
N optimal	25476
N conservative	25476
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.	0.1817
Phantom Peak	50
Corr. Phantom Peak	0.1842
Argmin. Corr.	1500
Min. Corr.	0.1613
NSC	1.1267
RSC	0.8939

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	0.1318

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	0.3068
AUC	0.4959
CHANCE divergence	0.0955
Elbow Point	0.0000
JS Distance	0.5812
Synthetic AUC	0.5056
Synthetic Elbow Point	0.1881
Synthetic JS Distance	0.2739