QC Report

	general
Report generated at	2019-11-22 15:04:04
Title	YJM789--YRR1
Description	chipseq of yeast YJM789 for tf YRR1
Pipeline version	v1.3.3
Pipeline type	tf
Genome	YJM789
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	6893598	5881750	5022862	7410926	11061052	8381776
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	5863958	4278943	3915768	5764661	8424118	5371312
Mapped Reads (QC-failed)	0	0	0	0	0	0
% Mapped Reads	85.1	72.7	78.0	77.8	76.2	64.1
Paired Reads	6893598	5881750	5022862	7410926	11061052	8381776
Paired Reads (QC-failed)	0	0	0	0	0	0
Read1	3446799	2940875	2511431	3705463	5530526	4190888
Read1 (QC-failed)	0	0	0	0	0	0
Read2	3446799	2940875	2511431	3705463	5530526	4190888
Read2 (QC-failed)	0	0	0	0	0	0
Properly Paired Reads	4755656	3351918	2796040	4317758	6012756	3063152
Properly Paired Reads (QC-failed)	0	0	0	0	0	0
% Properly Paired Reads	69.0	56.99999999999999	55.7	58.3	54.400000000000006	36.5
With itself	5721180	4162390	3839630	5654854	8256416	4415930
With itself (QC-failed)	0	0	0	0	0	0
Singletons	142778	116553	76138	109807	167702	955382
Singletons (QC-failed)	0	0	0	0	0	0
% Singleton	2.1	2.0	1.5	1.5	1.5	11.4
Diff. Chroms	2703	1922	1527	2704	3477	1976
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	1729011	1200977	1232537	1905255	2642866	1350940
Unmapped Reads	0	0	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0	0	0
Paired Duplicate Reads	79196	11504	3005	7226	12971	4196
Paired Optical Duplicate Reads	362	248	517	518	966	1248
% Duplicate Reads	4.5804	0.9579000000000001	0.24380000000000002	0.37929999999999997	0.4908	0.3106

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	3299630	2378946	2459064	3796058	5259790	2693488
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	3299630	2378946	2459064	3796058	5259790	2693488
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	3299630	2378946	2459064	3796058	5259790	2693488
Paired Reads (QC-failed)	0	0	0	0	0	0
Read1	1649815	1189473	1229532	1898029	2629895	1346744
Read1 (QC-failed)	0	0	0	0	0	0
Read2	1649815	1189473	1229532	1898029	2629895	1346744
Read2 (QC-failed)	0	0	0	0	0	0
Properly Paired Reads	3299630	2378946	2459064	3796058	5259790	2693488
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	3299630	2378946	2459064	3796058	5259790	2693488
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	1723162	1197444	1191364	1836406	2555651	1314860
Distinct Fragments	1644532	1186049	1188897	1830268	2544930	1311276
Positions with Two Read	72492	11056	2445	6088	10557	3566
NRF = Distinct/Total	0.954369	0.990484	0.997929	0.996658	0.995805	0.997274
PBC1 = OneRead/Distinct	0.954094	0.99054	0.997934	0.99666	0.99582	0.997274
PBC2 = OneRead/TwoRead	21.644292	106.261668	485.251943	299.631242	240.057971	366.713685

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	5093	489
N1	5548	449
N2	3570	448
Np	5426	455
N optimal	5426	489
N conservative	5093	489
Optimal Set	pooled-pr1_vs_pooled-pr2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.065383860200275	1.0747252747252747
Self Consistency Ratio	1.55406162464986	1.0022321428571428
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	10310	11837

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	69.0	73.0	75.0	75.0
25 percentile	270.0	260.0	234.0	296.0
50 percentile (median)	270.0	260.0	272.0	296.0
75 percentile	270.0	260.0	296.0	296.0
Max size	387.0	642.0	687.0	687.0
Mean	268.0069835111542	258.1594998732787	263.8732106339468	292.90950976778475

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	2283829	1691895
Estimated Fragment Length	120	125
Cross-correlation at Estimated Fragment Length	0.86076174960789	0.831755743786099
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.8595777	0.8308067
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.8403988	0.8059904
NSC (Normalized Strand Cross-correlation coeff.)	1.02423	1.031967
RSC (Relative Strand Cross-correlation coeff.)	1.061735	1.038241

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	0.4157220658073784	0.4696348719138644	0.47654950612674385	0.41980741067059896	0.47815268872733535	0.41913891205509674	0.38378741430950297	0.4395151604802609	0.4399842072971867

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	0.2584077416591765	0.2685879931992375	0.20783363724943735	0.2716957561191397

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	0.08364914020698147	0.07693953564490565	0.08228055617908099	0.08156094063018617

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