Untitled

No description

Report generated at 2020-06-10 18:45:16

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	104415760	208397864
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	103816876	205001725
Mapped(QC-failed)	0	0
% Mapped	99.4300	98.3700
Paired	104415760	208397864
Paired(QC-failed)	0	0
Read1	52207880	104198932
Read1(QC-failed)	0	0
Read2	52207880	104198932
Read2(QC-failed)	0	0
Properly Paired	103508855	199305552
Properly Paired(QC-failed)	0	0
% Properly Paired	99.1300	95.6400
With itself	103586642	203636967
With itself(QC-failed)	0	0
Singletons	230234	1364758
Singletons(QC-failed)	0	0
% Singleton	0.2200	0.6500
Diff. Chroms	16920	299406
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	49301725	87961925
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2676766	1539621
Paired Opt. Dupes	1847	2337
% Dupes/100	0.0543	0.0175

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49299263	87957322
Distinct Read Pairs	46622586	86418077
One Read Pair	44590608	84991683
Two Read Pairs	1686540	1357144
NRF = Distinct/Total	0.9457	0.9825
PBC1 = OnePair/Distinct	0.9564	0.9835
PBC2 = OnePair/TwoPair	26.4391	62.6254

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	93249918	172844608
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	93249918	172844608
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	93249918	172844608
Paired(QC-failed)	0	0
Read1	46624959	86422304
Read1(QC-failed)	0	0
Read2	46624959	86422304
Read2(QC-failed)	0	0
Properly Paired	93249918	172844608
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	93249918	172844608
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	124907
Np	0
N optimal	124907
N conservative	124907
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.	160
Corr. Est. Fragment Len.	0.3049
Phantom Peak	55
Corr. Phantom Peak	0.2246
Argmin. Corr.	1500
Min. Corr.	0.1858
NSC	1.6406
RSC	3.0747

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	0.7385

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	0.0645
AUC	0.4958
CHANCE divergence	0.3191
Elbow Point	0.0000
JS Distance	0.8702
Synthetic AUC	0.5015
Synthetic Elbow Point	0.5623
Synthetic JS Distance	0.6566