QC Report

	general
Report generated at	2019-12-05 23:07:02
Title	RM11-1A--PHD1
Description	chipseq of yeast RM11-1A for tf PHD1
Pipeline version	v1.3.3
Pipeline type	tf
Genome	RM11-1A
Paired-end per replicate	[True, True]
Aligner	bowtie2
Peak caller	spp
Control paired-end per replicate	[True, True, True, True, True]

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2	ctl3	ctl4	ctl5
Total Reads	5295866	5172572	5979138	6745678	13971978	12140748	10833130
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	3679926	3991960	5166983	6271325	12144083	10305567	7945377
Mapped Reads (QC-failed)	0	0	0	0	0	0	0
% Mapped Reads	69.5	77.2	86.4	93.0	86.9	84.89999999999999	73.3
Paired Reads	5295866	5172572	5979138	6745678	13971978	12140748	10833130
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	2647933	2586286	2989569	3372839	6985989	6070374	5416565
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	2647933	2586286	2989569	3372839	6985989	6070374	5416565
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	2905436	3291288	3869794	5089238	9132718	7699460	4827478
Properly Paired Reads (QC-failed)	0	0	0	0	0	0	0
% Properly Paired Reads	54.900000000000006	63.6	64.7	75.4	65.4	63.4	44.6
With itself	3597356	3885490	5084842	6190248	11938880	10133338	6728650
With itself (QC-failed)	0	0	0	0	0	0	0
Singletons	82570	106470	82141	81077	205203	172229	1216727
Singletons (QC-failed)	0	0	0	0	0	0	0
% Singleton	1.6	2.1	1.4000000000000001	1.2	1.5	1.4000000000000001	11.200000000000001
Diff. Chroms	1126	1969	2114	2798	6867	4103	2752
Diff. Chroms (QC-failed)	0	0	0	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2	ctl3	ctl4	ctl5
Unpaired Reads	0	0	0	0	0	0	0
Paired Reads	998951	1038121	1666318	2209745	3895451	3301669	2074939
Unmapped Reads	0	0	0	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0	0	0	0
Paired Duplicate Reads	10464	12173	4617	14267	24397	18211	8542
Paired Optical Duplicate Reads	254	280	672	595	1024	1240	2116
% Duplicate Reads	1.0475	1.1726	0.2771	0.6456	0.6263000000000001	0.5516	0.4117

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	ctl5
Total Reads	1976974	2051896	3323402	4390956	7742108	6566916	4132794
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	1976974	2051896	3323402	4390956	7742108	6566916	4132794
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	1976974	2051896	3323402	4390956	7742108	6566916	4132794
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	988487	1025948	1661701	2195478	3871054	3283458	2066397
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	988487	1025948	1661701	2195478	3871054	3283458	2066397
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	1976974	2051896	3323402	4390956	7742108	6566916	4132794
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	1976974	2051896	3323402	4390956	7742108	6566916	4132794
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	ctl1	ctl2	ctl3	ctl4	ctl5
Total Fragments	996323	1035458	1622980	2105576	3771782	3216376	2033094
Distinct Fragments	985921	1023334	1619228	2095316	3753321	3201528	2025906
Positions with Two Read	10013	11754	3655	10057	17329	14186	7012
NRF = Distinct/Total	0.98956	0.988291	0.997688	0.995127	0.995105	0.995384	0.996465
PBC1 = OneRead/Distinct	0.989652	0.988337	0.997713	0.995153	0.995246	0.995472	0.996497
PBC2 = OneRead/TwoRead	97.445221	86.047218	442.004104	207.334295	215.562294	224.66044	287.90773

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	1372	698
N1	1456	622
N2	1538	531
Np	1416	578
N optimal	1416	698
N conservative	1372	698
Optimal Set	pooled-pr1_vs_pooled-pr2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.032069970845481	1.207612456747405
Self Consistency Ratio	1.0563186813186813	1.1713747645951036
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	3488	4215

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	79.0	84.0	86.0	86.0
25 percentile	316.0	336.0	283.0	339.0
50 percentile (median)	316.0	336.0	342.0	344.0
75 percentile	316.0	336.0	350.0	344.0
Max size	708.0	754.0	798.0	798.0
Mean	307.0960435779817	329.74282325029657	318.8295128939828	329.441384180791

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	1423856	1278746
Estimated Fragment Length	105	170
Cross-correlation at Estimated Fragment Length	0.801343935700582	0.791546414470681
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.8002279	0.7810019
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7544516	0.7415504
NSC (Normalized Strand Cross-correlation coeff.)	1.062154	1.067421
RSC (Relative Strand Cross-correlation coeff.)	1.024381	1.267277

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	0.27753678095918305	0.3088241314374608	0.3123285259912108	0.3196273105459536	0.3155037097136429	0.31043873568640906	0.30773864632018405	0.27104559291037295	0.2748633114810413

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	0.18619786689568044	0.189054585442196	0.19828734009910834	0.19004435486873492

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	0.15013192284685284	0.1424909988699902	0.13638995348692137	0.14183381444424864

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