QC Report

	general
Report generated at	2019-12-06 19:45:59
Title	AWRI1631--SOK2
Description	chipseq of yeast AWRI1631 for tf SOK2
Pipeline version	v1.3.3
Pipeline type	tf
Genome	AWRI1631
Paired-end per replicate	[True, 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	rep3	ctl1	ctl2	ctl3	ctl4
Total Reads	7193582	5802464	5835950	5917546	6601090	11652572	8804978
Total Reads (QC-failed)	0	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0	0
Mapped Reads	6125352	4938327	5006374	4977004	5788309	9693515	6321027
Mapped Reads (QC-failed)	0	0	0	0	0	0	0
% Mapped Reads	85.2	85.1	85.8	84.1	87.7	83.2	71.8
Paired Reads	7193582	5802464	5835950	5917546	6601090	11652572	8804978
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	3596791	2901232	2917975	2958773	3300545	5826286	4402489
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	3596791	2901232	2917975	2958773	3300545	5826286	4402489
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	5222764	4132604	4130456	3717114	4357276	7216522	3826466
Properly Paired Reads (QC-failed)	0	0	0	0	0	0	0
% Properly Paired Reads	72.6	71.2	70.8	62.8	66.0	61.9	43.5
With itself	6050246	4833320	4908706	4894834	5693772	9527698	5338574
With itself (QC-failed)	0	0	0	0	0	0	0
Singletons	75106	105007	97668	82170	94537	165817	982453
Singletons (QC-failed)	0	0	0	0	0	0	0
% Singleton	1.0	1.7999999999999998	1.7000000000000002	1.4000000000000001	1.4000000000000001	1.4000000000000001	11.200000000000001
Diff. Chroms	2517	2099	2564	2445	2633	5103	2765
Diff. Chroms (QC-failed)	0	0	0	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	rep3	ctl1	ctl2	ctl3	ctl4
Unpaired Reads	0	0	0	0	0	0	0
Paired Reads	2237884	1566732	1449655	1618488	1908814	3134719	1665993
Unmapped Reads	0	0	0	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0	0	0	0
Paired Duplicate Reads	26672	12116	11386	4666	7580	17416	5903
Paired Optical Duplicate Reads	767	441	290	658	501	1171	1570
% Duplicate Reads	1.1918	0.7733	0.7854	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	rep3	ctl1	ctl2	ctl3	ctl4
Total Reads	4422424	3109232	2876538	3227644	3802468	6234606	3320180
Total Reads (QC-failed)	0	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0	0
Mapped Reads	4422424	3109232	2876538	3227644	3802468	6234606	3320180
Mapped Reads (QC-failed)	0	0	0	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0	100.0	100.0	100.0
Paired Reads	4422424	3109232	2876538	3227644	3802468	6234606	3320180
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	2211212	1554616	1438269	1613822	1901234	3117303	1660090
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	2211212	1554616	1438269	1613822	1901234	3117303	1660090
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	4422424	3109232	2876538	3227644	3802468	6234606	3320180
Properly Paired Reads (QC-failed)	0	0	0	0	0	0	0
% Properly Paired Reads	100.0	100.0	100.0	100.0	100.0	100.0	100.0
With itself	4422424	3109232	2876538	3227644	3802468	6234606	3320180
With itself (QC-failed)	0	0	0	0	0	0	0
Singletons	0	0	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0	0	0
Diff. Chroms (QC-failed)	0	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	rep3	ctl1	ctl2	ctl3	ctl4
Total Fragments	2235038	1563634	1447139	1571325	1852755	3044551	1629062
Distinct Fragments	2208481	1551589	1435837	1567386	1846120	3029617	1623881
Positions with Two Read	25591	11772	10957	3865	6528	14432	5101
NRF = Distinct/Total	0.988118	0.992297	0.99219	0.997493	0.996419	0.995095	0.99682
PBC1 = OneRead/Distinct	0.988199	0.992328	0.992251	0.997511	0.996436	0.995157	0.996835
PBC2 = OneRead/TwoRead	85.280685	130.792134	130.02738	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	2528	1008
N1	3017	963
N2	1873	847
N3	2237	880
Np	2840	1020
N optimal	2840	1020
N conservative	2528	1008
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep3	rep2_vs_rep3
Rescue Ratio	1.1234177215189873	1.0119047619047619
Self Consistency Ratio	1.610784837159637	1.1369539551357732
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	rep3
Number of peaks	4227	3966	5064

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	rep3	idr_opt	overlap_opt
Min size	134.0	100.0	100.0	124.0	122.0
25 percentile	536.0	400.0	400.0	354.75	490.0
50 percentile (median)	536.0	400.0	400.0	490.0	490.0
75 percentile	536.0	400.0	400.0	601.0	490.0
Max size	2212.0	1384.0	2106.0	2240.0	2240.0
Mean	525.9190915542938	388.1391830559758	391.5416666666667	560.928431372549	511.0292253521127

Enrichment / Signal-to-noise ratio

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

	rep1	rep2	rep3
Number of Subsampled Reads	2790762	1889952	1853473
Estimated Fragment Length	145	160	155
Cross-correlation at Estimated Fragment Length	0.890449979685426	0.848786627162171	0.847123165259529
Phantom Peak	55	55	50
Cross-correlation at Phantom Peak	0.885676	0.8412068	0.8406134
Argmin of Cross-correlation	1500	1500	1500
Minimum of Cross-correlation	0.852198	0.8042605	0.8024314
NSC (Normalized Strand Cross-correlation coeff.)	1.044886	1.055363	1.055695
RSC (Relative Strand Cross-correlation coeff.)	1.142599	1.205157	1.170493

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	rep3	rep1-pr1	rep2-pr1	rep3-pr1	rep1-pr2	rep2-pr2	rep3-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.3370515807620436	0.30868490997133696	0.34599369102720007	0.3652046931727939	0.317845049838674	0.34895673274141853	0.384042778349611	0.31324069738121824	0.3456747977428407	0.29331851423983835	0.31366742132834546	0.32144603020390095

FRiP for overlap peaks

	rep1_vs_rep2	rep1_vs_rep3	rep2_vs_rep3	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	rep3-pr1_vs_rep3-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.24672906750200851	0.2548665983743193	0.25107439388620156	0.29456696146728584	0.2229872199951628	0.24455821546595247	0.2714118318701592

FRiP for IDR peaks

	rep1_vs_rep2	rep1_vs_rep3	rep2_vs_rep3	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	rep3-pr1_vs_rep3-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.17703657329984435	0.18227033431544415	0.18431343612542195	0.18497389666843342	0.16021223247412866	0.16497504986897443	0.1859649234055399

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