Untitled

No description

Report generated at 2020-07-14 22:54:10

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	77404254	62419198
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	65613774	59332530
Mapped(QC-failed)	0	0
% Mapped	84.7700	95.0500
Paired	77404254	62419198
Paired(QC-failed)	0	0
Read1	38702127	31209599
Read1(QC-failed)	0	0
Read2	38702127	31209599
Read2(QC-failed)	0	0
Properly Paired	57372754	52460965
Properly Paired(QC-failed)	0	0
% Properly Paired	74.1200	84.0500
With itself	62697818	57668794
With itself(QC-failed)	0	0
Singletons	2915956	1663736
Singletons(QC-failed)	0	0
% Singleton	3.7700	2.6700
Diff. Chroms	2648028	3447531
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	21596728	21847315
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	742336	249453
Paired Opt. Dupes	1916	2581
% Dupes/100	0.0344	0.0114

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	21585285	21831616
Distinct Read Pairs	20843392	21582603
One Read Pair	20122653	21335971
Two Read Pairs	700106	244266
NRF = Distinct/Total	0.9656	0.9886
PBC1 = OnePair/Distinct	0.9654	0.9886
PBC2 = OnePair/TwoPair	28.7423	87.3473

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	41708784	43195724
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	41708784	43195724
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	41708784	43195724
Paired(QC-failed)	0	0
Read1	20854392	21597862
Read1(QC-failed)	0	0
Read2	20854392	21597862
Read2(QC-failed)	0	0
Properly Paired	41708784	43195724
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	41708784	43195724
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	71333
Np	0
N optimal	71333
N conservative	71333
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.	240
Corr. Est. Fragment Len.	0.2134
Phantom Peak	50
Corr. Phantom Peak	0.2401
Argmin. Corr.	1500
Min. Corr.	0.1920
NSC	1.1113
RSC	0.4438

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	0.1237

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	0.1822
AUC	0.4936
CHANCE divergence	0.2426
Elbow Point	0.0000
JS Distance	0.6630
Synthetic AUC	0.4949
Synthetic Elbow Point	0.1022
Synthetic JS Distance	0.3861