Untitled

No description

Report generated at 2020-06-10 16:11:55

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	126208740	123436302
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	124254730	121216389
Mapped(QC-failed)	0	0
% Mapped	98.4500	98.2000
Paired	126208740	123436302
Paired(QC-failed)	0	0
Read1	63104370	61718151
Read1(QC-failed)	0	0
Read2	63104370	61718151
Read2(QC-failed)	0	0
Properly Paired	122652462	118424048
Properly Paired(QC-failed)	0	0
% Properly Paired	97.1800	95.9400
With itself	123193422	120225855
With itself(QC-failed)	0	0
Singletons	1061308	990534
Singletons(QC-failed)	0	0
% Singleton	0.8400	0.8000
Diff. Chroms	157426	233679
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	54074348	52405522
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	732991	353361
Paired Opt. Dupes	3263	2501
% Dupes/100	0.0136	0.0067

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	54062245	52322111
Distinct Read Pairs	53329453	51995463
One Read Pair	52607650	51683877
Two Read Pairs	711636	305227
NRF = Distinct/Total	0.9864	0.9938
PBC1 = OnePair/Distinct	0.9865	0.9940
PBC2 = OnePair/TwoPair	73.9249	169.3293

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	106682714	104104322
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	106682714	104104322
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	106682714	104104322
Paired(QC-failed)	0	0
Read1	53341357	52052161
Read1(QC-failed)	0	0
Read2	53341357	52052161
Read2(QC-failed)	0	0
Properly Paired	106682714	104104322
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	106682714	104104322
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	109010
Np	0
N optimal	109010
N conservative	109010
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.	145
Corr. Est. Fragment Len.	0.1783
Phantom Peak	50
Corr. Phantom Peak	0.1833
Argmin. Corr.	1500
Min. Corr.	0.1737
NSC	1.0264
RSC	0.4805

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	0.1265

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	0.2785
AUC	0.4961
CHANCE divergence	0.0980
Elbow Point	0.0000
JS Distance	0.6052
Synthetic AUC	0.5026
Synthetic Elbow Point	0.1016
Synthetic JS Distance	0.2850