QC Report

	general
Report generated at	2019-12-07 11:48:09
Title	AWRI1631--PHD1
Description	chipseq of yeast AWRI1631 for tf PHD1
Pipeline version	v1.3.3
Pipeline type	tf
Genome	AWRI1631
Paired-end per replicate	[True, True]
Aligner	bowtie2
Peak caller	spp
Control paired-end per replicate	[True, True, True, True]

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2	ctl3	ctl4
Total Reads	5944464	6256076	5917546	6601090	11652572	8804978
Total Reads (QC-failed)	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0
Mapped Reads	4494863	4302044	4977004	5788309	9693515	6321027
Mapped Reads (QC-failed)	0	0	0	0	0	0
% Mapped Reads	75.6	68.8	84.1	87.7	83.2	71.8
Paired Reads	5944464	6256076	5917546	6601090	11652572	8804978
Paired Reads (QC-failed)	0	0	0	0	0	0
Read1	2972232	3128038	2958773	3300545	5826286	4402489
Read1 (QC-failed)	0	0	0	0	0	0
Read2	2972232	3128038	2958773	3300545	5826286	4402489
Read2 (QC-failed)	0	0	0	0	0	0
Properly Paired Reads	3779088	3359926	3717114	4357276	7216522	3826466
Properly Paired Reads (QC-failed)	0	0	0	0	0	0
% Properly Paired Reads	63.6	53.7	62.8	66.0	61.9	43.5
With itself	4433828	4168398	4894834	5693772	9527698	5338574
With itself (QC-failed)	0	0	0	0	0	0
Singletons	61035	133646	82170	94537	165817	982453
Singletons (QC-failed)	0	0	0	0	0	0
% Singleton	1.0	2.1	1.4000000000000001	1.4000000000000001	1.4000000000000001	11.200000000000001
Diff. Chroms	1722	2025	2445	2633	5103	2765
Diff. Chroms (QC-failed)	0	0	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2	ctl3	ctl4
Unpaired Reads	0	0	0	0	0	0
Paired Reads	1561982	1148505	1618488	1908814	3134719	1665993
Unmapped Reads	0	0	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0	0	0
Paired Duplicate Reads	21347	10649	4666	7580	17416	5903
Paired Optical Duplicate Reads	508	310	658	501	1171	1570
% Duplicate Reads	1.3667	0.9272	0.2883	0.39709999999999995	0.5556	0.3543

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	ctl2	ctl3	ctl4
Total Reads	3081270	2275712	3227644	3802468	6234606	3320180
Total Reads (QC-failed)	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0
Mapped Reads	3081270	2275712	3227644	3802468	6234606	3320180
Mapped Reads (QC-failed)	0	0	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0	100.0	100.0
Paired Reads	3081270	2275712	3227644	3802468	6234606	3320180
Paired Reads (QC-failed)	0	0	0	0	0	0
Read1	1540635	1137856	1613822	1901234	3117303	1660090
Read1 (QC-failed)	0	0	0	0	0	0
Read2	1540635	1137856	1613822	1901234	3117303	1660090
Read2 (QC-failed)	0	0	0	0	0	0
Properly Paired Reads	3081270	2275712	3227644	3802468	6234606	3320180
Properly Paired Reads (QC-failed)	0	0	0	0	0	0
% Properly Paired Reads	100.0	100.0	100.0	100.0	100.0	100.0
With itself	3081270	2275712	3227644	3802468	6234606	3320180
With itself (QC-failed)	0	0	0	0	0	0
Singletons	0	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0	0
Diff. Chroms (QC-failed)	0	0	0	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	ctl2	ctl3	ctl4
Total Fragments	1559335	1144560	1571325	1852755	3044551	1629062
Distinct Fragments	1538092	1133997	1567386	1846120	3029617	1623881
Positions with Two Read	20350	10122	3865	6528	14432	5101
NRF = Distinct/Total	0.986377	0.990771	0.997493	0.996419	0.995095	0.99682
PBC1 = OneRead/Distinct	0.986491	0.99089	0.997511	0.996436	0.995157	0.996835
PBC2 = OneRead/TwoRead	74.560885	111.012251	404.523674	281.792279	208.906943	317.337973

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	2327	726
N1	2288	813
N2	1555	588
Np	2513	814
N optimal	2513	814
N conservative	2327	726
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0799312419424152	1.121212121212121
Self Consistency Ratio	1.4713826366559486	1.3826530612244898
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	7724	3765

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	104.0	90.0	98.0	98.0
25 percentile	416.0	360.0	277.25	390.0
50 percentile (median)	416.0	360.0	330.5	390.0
75 percentile	416.0	360.0	390.0	390.0
Max size	1183.0	815.0	1212.0	1212.0
Mean	407.8634127395132	348.3925630810093	337.5933660933661	371.7349781138082

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	2057005	1652168
Estimated Fragment Length	145	110
Cross-correlation at Estimated Fragment Length	0.864709989875869	0.824563339654161
Phantom Peak	50	55
Cross-correlation at Phantom Peak	0.862557	0.8210219
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.8424458	0.7838843
NSC (Normalized Strand Cross-correlation coeff.)	1.026428	1.051894
RSC (Relative Strand Cross-correlation coeff.)	1.107055	1.095359

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

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

	rep1	rep2	rep1-pr1	rep2-pr1	rep1-pr2	rep2-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.38942708688300604	0.2939339424320828	0.3118854810610683	0.30520382192474266	0.3293046888488765	0.30500696045896847	0.3056106964705127	0.31081817679500257	0.309798431205642

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	0.19305291673557984	0.19132890009638884	0.1984095527026267	0.20987862195542192

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	0.11001829014919222	0.10761731364015487	0.13753761460149616	0.12584212528621527

For spp 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