Untitled

No description

Report generated at 2020-07-14 16:30:08

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	82756042	55171578
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	66664873	47068616
Mapped(QC-failed)	0	0
% Mapped	80.5600	85.3100
Paired	82756042	55171578
Paired(QC-failed)	0	0
Read1	41378021	27585789
Read1(QC-failed)	0	0
Read2	41378021	27585789
Read2(QC-failed)	0	0
Properly Paired	62820006	35347907
Properly Paired(QC-failed)	0	0
% Properly Paired	75.9100	64.0700
With itself	64192050	44252789
With itself(QC-failed)	0	0
Singletons	2472823	2815827
Singletons(QC-failed)	0	0
% Singleton	2.9900	5.1000
Diff. Chroms	680717	5846632
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	26126719	12506303
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	685319	404677
Paired Opt. Dupes	2104	2144
% Dupes/100	0.0262	0.0324

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	26111454	12503649
Distinct Read Pairs	25426550	12099064
One Read Pair	24756535	11706385
Two Read Pairs	655418	381329
NRF = Distinct/Total	0.9738	0.9676
PBC1 = OnePair/Distinct	0.9736	0.9675
PBC2 = OnePair/TwoPair	37.7721	30.6989

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	50882800	24203252
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	50882800	24203252
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	50882800	24203252
Paired(QC-failed)	0	0
Read1	25441400	12101626
Read1(QC-failed)	0	0
Read2	25441400	12101626
Read2(QC-failed)	0	0
Properly Paired	50882800	24203252
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	50882800	24203252
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	69053
Np	0
N optimal	69053
N conservative	69053
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.	275
Corr. Est. Fragment Len.	0.1991
Phantom Peak	50
Corr. Phantom Peak	0.2141
Argmin. Corr.	1500
Min. Corr.	0.1833
NSC	1.0864
RSC	0.5144

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	0.0971

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	0.1887
AUC	0.4942
CHANCE divergence	0.2434
Elbow Point	0.0000
JS Distance	0.6426
Synthetic AUC	0.5017
Synthetic Elbow Point	0.0861
Synthetic JS Distance	0.3771