Untitled

No description

Report generated at 2020-05-18 01:03:42

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	79827642	91058302
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	77663730	88858777
Mapped(QC-failed)	0	0
% Mapped	97.2900	97.5800
Paired	79827642	91058302
Paired(QC-failed)	0	0
Read1	39913821	45529151
Read1(QC-failed)	0	0
Read2	39913821	45529151
Read2(QC-failed)	0	0
Properly Paired	76925656	87463672
Properly Paired(QC-failed)	0	0
% Properly Paired	96.3600	96.0500
With itself	77415532	88414762
With itself(QC-failed)	0	0
Singletons	248198	444015
Singletons(QC-failed)	0	0
% Singleton	0.3100	0.4900
Diff. Chroms	299018	473257
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	35613210	38226012
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	218620	140477
Paired Opt. Dupes	1238	1407
% Dupes/100	0.0061	0.0037

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	35608886	38152882
Distinct Read Pairs	35390292	38013834
One Read Pair	35173042	37875216
Two Read Pairs	215911	138191
NRF = Distinct/Total	0.9939	0.9964
PBC1 = OnePair/Distinct	0.9939	0.9964
PBC2 = OnePair/TwoPair	162.9053	274.0787

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	70789180	76171070
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	70789180	76171070
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	70789180	76171070
Paired(QC-failed)	0	0
Read1	35394590	38085535
Read1(QC-failed)	0	0
Read2	35394590	38085535
Read2(QC-failed)	0	0
Properly Paired	70789180	76171070
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	70789180	76171070
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	125784
Np	0
N optimal	125784
N conservative	125784
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.	190
Corr. Est. Fragment Len.	0.2147
Phantom Peak	50
Corr. Phantom Peak	0.2117
Argmin. Corr.	1500
Min. Corr.	0.1932
NSC	1.1113
RSC	1.1617

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	0.4337

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	0.1543
AUC	0.4952
CHANCE divergence	0.1750
Elbow Point	0.0000
JS Distance	0.7599
Synthetic AUC	0.4974
Synthetic Elbow Point	0.3048
Synthetic JS Distance	0.4797