Untitled

No description

Report generated at 2019-11-01 08:20:32

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	88746074	317909612
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	87717933	312072580
Mapped(QC-failed)	0	0
% Mapped	98.8400	98.1600
Paired	88746074	317909612
Paired(QC-failed)	0	0
Read1	44373037	158954806
Read1(QC-failed)	0	0
Read2	44373037	158954806
Read2(QC-failed)	0	0
Properly Paired	85010012	294728580
Properly Paired(QC-failed)	0	0
% Properly Paired	95.7900	92.7100
With itself	87204037	309884253
With itself(QC-failed)	0	0
Singletons	513896	2188327
Singletons(QC-failed)	0	0
% Singleton	0.5800	0.6900
Diff. Chroms	1087235	9012143
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	34916888	121497414
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	5702646	13623598
Paired Opt. Dupes	14251	34172
% Dupes/100	0.1633	0.1121

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34915825	121417759
Distinct Read Pairs	29213334	107806572
One Read Pair	24335360	95829671
Two Read Pairs	4161811	10543184
NRF = Distinct/Total	0.8367	0.8879
PBC1 = OnePair/Distinct	0.8330	0.8889
PBC2 = OnePair/TwoPair	5.8473	9.0893

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	58428484	215747632
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	58428484	215747632
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	58428484	215747632
Paired(QC-failed)	0	0
Read1	29214242	107873816
Read1(QC-failed)	0	0
Read2	29214242	107873816
Read2(QC-failed)	0	0
Properly Paired	58428484	215747632
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	58428484	215747632
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	123714
Np	0
N optimal	123714
N conservative	123714
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.	195
Corr. Est. Fragment Len.	0.1616
Phantom Peak	50
Corr. Phantom Peak	0.1678
Argmin. Corr.	1500
Min. Corr.	0.1583
NSC	1.0213
RSC	0.3537

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	0.1102

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	0.2601
AUC	0.4935
CHANCE divergence	0.1359
Elbow Point	0.0000
JS Distance	0.5865
Synthetic AUC	0.4979
Synthetic Elbow Point	0.1859
Synthetic JS Distance	0.2904