QC Report

	general
Report generated at	2019-11-20 14:05:24
Title	AWRI1631--HAA1
Description	chipseq of yeast AWRI1631 for tf HAA1
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	6969416	6058706	5609032	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	3773336	4286322	4934620	4977004	5788309	9693515	6321027
Mapped Reads (QC-failed)	0	0	0	0	0	0	0
% Mapped Reads	54.1	70.7	88.0	84.1	87.7	83.2	71.8
Paired Reads	6969416	6058706	5609032	5917546	6601090	11652572	8804978
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	3484708	3029353	2804516	2958773	3300545	5826286	4402489
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	3484708	3029353	2804516	2958773	3300545	5826286	4402489
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	3097974	3396524	4074020	3717114	4357276	7216522	3826466
Properly Paired Reads (QC-failed)	0	0	0	0	0	0	0
% Properly Paired Reads	44.5	56.10000000000001	72.6	62.8	66.0	61.9	43.5
With itself	3719824	4162926	4836180	4894834	5693772	9527698	5338574
With itself (QC-failed)	0	0	0	0	0	0	0
Singletons	53512	123396	98440	82170	94537	165817	982453
Singletons (QC-failed)	0	0	0	0	0	0	0
% Singleton	0.8	2.0	1.7999999999999998	1.4000000000000001	1.4000000000000001	1.4000000000000001	11.200000000000001
Diff. Chroms	927	1864	2517	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	1295532	1042028	1259224	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	21167	15573	13508	4666	7580	17416	5903
Paired Optical Duplicate Reads	357	289	266	658	501	1171	1570
% Duplicate Reads	1.6338	1.4945	1.0727	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	2548730	2052910	2491432	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	2548730	2052910	2491432	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	2548730	2052910	2491432	3227644	3802468	6234606	3320180
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	1274365	1026455	1245716	1613822	1901234	3117303	1660090
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	1274365	1026455	1245716	1613822	1901234	3117303	1660090
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	2548730	2052910	2491432	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	2548730	2052910	2491432	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	1291531	1034996	1255786	1571325	1852755	3044551	1629062
Distinct Fragments	1270488	1019599	1242366	1567386	1846120	3029617	1623881
Positions with Two Read	20393	14761	13060	3865	6528	14432	5101
NRF = Distinct/Total	0.983707	0.985124	0.989313	0.997493	0.996419	0.995095	0.99682
PBC1 = OneRead/Distinct	0.983694	0.985218	0.989345	0.997511	0.996436	0.995157	0.996835
PBC2 = OneRead/TwoRead	61.284362	68.052774	94.113936	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	4586	401
N1	7547	355
N2	1391	465
N3	4706	389
Np	5381	430
N optimal	5381	430
N conservative	4586	401
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep3	rep2_vs_rep3
Rescue Ratio	1.1733536851286523	1.0723192019950125
Self Consistency Ratio	5.425593098490295	1.3098591549295775
Reproducibility Test	borderline	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	14403	5696	11543

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	75.0	80.0	79.0	86.0	86.0
25 percentile	300.0	320.0	310.0	271.0	336.0
50 percentile (median)	300.0	320.0	310.0	298.0	336.0
75 percentile	300.0	320.0	310.0	333.0	336.0
Max size	510.0	728.0	624.0	733.0	733.0
Mean	299.8558633617996	317.17661516853934	307.5428398163389	295.8139534883721	332.65917115777734

Enrichment / Signal-to-noise ratio

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

	rep1	rep2	rep3
Number of Subsampled Reads	1821206	1350376	1593186
Estimated Fragment Length	110	140	130
Cross-correlation at Estimated Fragment Length	0.85157920368835	0.794249171030564	0.828561932125318
Phantom Peak	55	55	55
Cross-correlation at Phantom Peak	0.851853	0.7888424	0.8250501
Argmin of Cross-correlation	1500	1500	1500
Minimum of Cross-correlation	0.8437449	0.7478977	0.8068643
NSC (Normalized Strand Cross-correlation coeff.)	1.009285	1.061976	1.026891
RSC (Relative Strand Cross-correlation coeff.)	0.966228	1.132052	1.19311

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	0.552262107010158	0.34179871499481224	0.4784625869780913	0.5672075369242431	0.315086082598767	0.47751092544368057	0.5694518991434159	0.3051037844852278	0.48930012940349166	0.36963772537484463	0.44462007738250653	0.4422221808672918

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	0.16234742858947435	0.22062387072907197	0.16854657615205373	0.3282466169425557	0.1737450740655947	0.25178050213692366	0.268440106064058

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	0.05292657398656041	0.04613840096364453	0.07008134134265097	0.03458899138002064	0.1247716655868986	0.06876326546339614	0.0728828073365109

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