QC Report

	general
Report generated at	2020-03-28 20:45:39
Title	cbf1_pbexo
Description	pb exo data for cbf1
Pipeline version	v1.3.6
Pipeline type	tf
Genome	sacCer3
Aligner	bowtie2
Sequencing endedness	{'rep1': {'paired_end': True}, 'rep2': {'paired_end': True}, 'ctl1': {'paired_end': False}}
Peak caller	macs2

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1
Total Reads	5905048	6395296	6055441
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	4330014	4490268	5615958
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	73.3	70.19999999999999	92.7
Paired Reads	5905048	6395296	0
Paired Reads (QC-failed)	0	0	0
Read1	2952524	3197648	0
Read1 (QC-failed)	0	0	0
Read2	2952524	3197648	0
Read2 (QC-failed)	0	0	0
Properly Paired Reads	2961482	2898760	0
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	50.2	45.300000000000004	0.0
With itself	3890942	3990882	0
With itself (QC-failed)	0	0	0
Singletons	439072	499386	0
Singletons (QC-failed)	0	0	0
% Singleton	7.3999999999999995	7.8	0.0
Diff. Chroms	420171	479352	0
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	4971580
Paired Reads	1279270	1248144	0
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	1717069
Paired Duplicate Reads	1270542	1239502	0
Paired Optical Duplicate Reads	0	0	0
% Duplicate Reads	99.3177	99.3076	34.5377

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8, for paired-end)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

SAMstat (filtered/deduped BAM)

	rep1	rep2	ctl1
Total Reads	17456	17284	3254511
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	17456	17284	3254511
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	17456	17284	0
Paired Reads (QC-failed)	0	0	0
Read1	8728	8642	0
Read1 (QC-failed)	0	0	0
Read2	8728	8642	0
Read2 (QC-failed)	0	0	0
Properly Paired Reads	17456	17284	0
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	0.0
With itself	17456	17284	0
With itself (QC-failed)	0	0	0
Singletons	0	0	0
Singletons (QC-failed)	0	0	0
% Singleton	0.0	0.0	0.0
Diff. Chroms	0	0	0
Diff. Chroms (QC-failed)	0	0	0

Filtered and duplicates removed

Sequence quality metrics (filtered/deduped BAM)

Open chromatin assays are known to have significant GC bias. Please take this into consideration as necessary.

Library complexity quality metrics

Library complexity (filtered non-mito BAM)

	rep1	rep2	ctl1
Total Fragments	1258517	1226663	4962084
Distinct Fragments	8544	8446	3247815
Positions with Two Read	265	253	586396
NRF = Distinct/Total	0.006789	0.006885	0.654526
PBC1 = OneRead/Distinct	0.173104	0.153801	0.747173
PBC2 = OneRead/TwoRead	5.581132	5.134387	4.138296

Mitochondrial reads are filtered out by default. The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads in a dataset; it is the ratio between the number of positions in the genome that uniquely mapped reads map to and the total number of uniquely mappable reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with AT LEAST one read pair. PBC1 is the primary measure, and the PBC1 should be close to 1. Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking, 0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with EXACTLY two read pairs. The PBC2 should be significantly greater than 1. See more details at the ENCODE portal standard for ChIP-Seq pipeline

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

Replication quality metrics

IDR (Irreproducible Discovery Rate) plots

Reproducibility QC and peak detection statistics

	overlap	idr
Nt	380	125
N1	512	155
N2	557	147
Np	373	138
N optimal	380	138
N conservative	380	125
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0187667560321716	1.104
Self Consistency Ratio	1.087890625	1.054421768707483
Reproducibility Test	pass	pass

Reproducibility QC

N1: Replicate 1 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Ni: Replicate i self-consistent peaks (comparing two pseudoreplicates generated by subsampling RepX reads)
Nt: True Replicate consistent peaks (comparing true replicates Rep1 vs Rep2)
Np: Pooled-pseudoreplicate consistent 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'

Number of raw peaks

	rep1	rep2
Number of peaks	998	1031

Top 500000 raw peaks from macs2 with p-val threshold 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	150.0	150.0	191.0	150.0
25 percentile	157.0	156.0	479.5	284.0
50 percentile (median)	205.0	206.0	577.0	400.0
75 percentile	302.5	292.0	678.75	552.0
Max size	1327.0	1402.0	1443.0	1509.0
Mean	265.03206412825654	262.12221144519884	595.7028985507246	440.5763157894737

Enrichment / Signal-to-noise ratio

Strand cross-correlation measures (trimmed/filtered SE BAM)

	rep1	rep2
Number of Subsampled Reads	1945726	2028627
Estimated Fragment Length	90	60
Cross-correlation at Estimated Fragment Length	0.0367953173366808	0.0405572565138573
Phantom Peak	30	30
Cross-correlation at Phantom Peak	0.05749803	0.05629867
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.01860211	0.02017032
NSC (Normalized Strand Cross-correlation coeff.)	1.978018	2.010739
RSC (Relative Strand Cross-correlation coeff.)	0.4677408	0.5642919

Performed on subsampled (15000000) reads mapped from FASTQs that are trimmed to 50. Such FASTQ trimming and subsampling reads are for cross-corrleation analysis only. Untrimmed FASTQs are used for all the other analyses.

NOTE1: For SE datasets, reads from replicates are randomly subsampled to 15000000.
NOTE2: For PE datasets, the first end (R1) of each read-pair is selected and trimmed to 50 the reads are then randomly subsampled to 15000000.

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

Jensen-Shannon distance (filtered/deduped BAM)

	rep1	rep2
AUC	0.06671688668922404	0.06630776733375103
Synthetic AUC	0.4735922013623244	0.47347065353578943
X-intercept	0.7377542438372278	0.7397916068672181
Synthetic X-intercept	1.0661529032413551e-11	1.3718940192950028e-11
Elbow Point	0.7545569688855523	0.7564819256794054
Synthetic Elbow Point	0.5009981421360867	0.5205188974529715
JS Distance	0.32504076827259254	0.32240906051992585
Synthetic JS Distance	0.3518992710805833	0.3493533984723314
% Genome Enriched	24.49311812891791	24.295403588569087
Diff. Enrichment	73.31374260078141	73.63336606646227
CHANCE Divergence	0.7115841502757698	0.7138744260053081

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for macs2 raw peaks

	rep1	rep2	rep1-pr1	rep2-pr1	rep1-pr2	rep2-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.5323098075160403	0.5321106225410784	0.8943629697525206	0.8952788706317982	0.8935609532538955	0.8913445961582966	0.5228267127230858	0.5591249280368451	0.5533678756476684

FRiP for overlap peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.39723661485319517	0.4285632447296059	0.4311501967137237	0.39438687392055266

FRiP for IDR peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.28261370178468626	0.303448670944088	0.2849456144411016	0.2947898675877951

For macs2 raw peaks:

repX: Peak from true replicate X
repX-prY: Peak from Yth pseudoreplicates from replicate X
pooled: Peak from pooled true replicates (pool of rep1, rep2, ...)
pooled-pr1: Peak from 1st pooled pseudo replicate (pool of rep1-pr1, rep2-pr1, ...)
pooled-pr2: Peak from 2nd pooled pseudo replicate (pool of rep1-pr2, rep2-pr2, ...)

For overlap/IDR peaks:

repX_vs_repY: Comparing two peaks from true replicates X and Y
repX-pr1_vs_repX-pr2: Comparing two peaks from both pseudoreplicates from replicate X
pooled-pr1_vs_pooled-pr2: Comparing two peaks from 1st and 2nd pooled pseudo replicates