QC Report

	general
Report generated at	2020-03-28 21:33:46
Title	cbf1_exo
Description	chip exo data for cbf1
Pipeline version	v1.3.6
Pipeline type	tf
Genome	sacCer3
Aligner	bowtie2
Sequencing endedness	{'rep1': {'paired_end': True}, 'rep2': {'paired_end': True}, 'rep3': {'paired_end': True}, 'rep4': {'paired_end': True}, 'rep5': {'paired_end': True}, 'ctl1': {'paired_end': True}, 'ctl2': {'paired_end': True}}
Peak caller	macs2

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	rep3	rep4	rep5	ctl1	ctl2
Total Reads	4043738	5881436	10724954	15517140	22852794	3555302	2475684
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	3385525	5065939	7498001	11500787	17619715	1729789	2119384
Mapped Reads (QC-failed)	0	0	0	0	0	0	0
% Mapped Reads	83.7	86.1	69.89999999999999	74.1	77.10000000000001	48.699999999999996	85.6
Paired Reads	4043738	5881436	10724954	15517140	22852794	3555302	2475684
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	2021869	2940718	5362477	7758570	11426397	1777651	1237842
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	2021869	2940718	5362477	7758570	11426397	1777651	1237842
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	2903686	4449376	5708174	9090010	14376380	1624258	1980632
Properly Paired Reads (QC-failed)	0	0	0	0	0	0	0
% Properly Paired Reads	71.8	75.7	53.2	58.599999999999994	62.9	45.7	80.0
With itself	3022962	4648518	5761984	9152710	14508610	1628458	1982620
With itself (QC-failed)	0	0	0	0	0	0	0
Singletons	362563	417421	1736017	2348077	3111105	101331	136764
Singletons (QC-failed)	0	0	0	0	0	0	0
% Singleton	9.0	7.1	16.2	15.1	13.600000000000001	2.9000000000000004	5.5
Diff. Chroms	44162	81578	17638	22493	49992	546	783
Diff. Chroms (QC-failed)	0	0	0	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	rep3	rep4	rep5	ctl1	ctl2
Unpaired Reads	0	0	0	0	0	0	0
Paired Reads	1166618	1761628	2359204	3682334	5847109	581306	779111
Unmapped Reads	0	0	0	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0	0	0	0
Paired Duplicate Reads	997753	1547855	1352510	2751052	3815264	551622	738554
Paired Optical Duplicate Reads	0	0	0	0	0	0	0
% Duplicate Reads	85.5253	87.86500000000001	57.3291	74.70949999999999	65.2504	94.8936	94.7945

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	rep4	rep5	ctl1	ctl2
Total Reads	337730	427546	2013388	1862564	4063690	59368	81114
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	337730	427546	2013388	1862564	4063690	59368	81114
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	337730	427546	2013388	1862564	4063690	59368	81114
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	168865	213773	1006694	931282	2031845	29684	40557
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	168865	213773	1006694	931282	2031845	29684	40557
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	337730	427546	2013388	1862564	4063690	59368	81114
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	337730	427546	2013388	1862564	4063690	59368	81114
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	rep4	rep5	ctl1	ctl2
Total Fragments	1165780	1760662	2355127	3677849	5841981	579915	776487
Distinct Fragments	168745	213649	1004926	930157	2029912	29612	40375
Positions with Two Read	26349	32647	250825	164653	462946	1244	1466
NRF = Distinct/Total	0.144749	0.121346	0.426697	0.252908	0.34747	0.051063	0.051997
PBC1 = OneRead/Distinct	0.267107	0.252863	0.407107	0.234843	0.315362	0.068722	0.065684
PBC2 = OneRead/TwoRead	1.710615	1.654792	1.631065	1.326675	1.38279	1.635852	1.809004

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	137	124
N1	250	142
N2	274	127
N3	92	40
N4	130	80
N5	106	88
Np	132	91
N optimal	137	124
N conservative	137	124
Optimal Set	rep1_vs_rep2	rep2_vs_rep4
Conservative Set	rep1_vs_rep2	rep2_vs_rep4
Rescue Ratio	1.0378787878787878	1.3626373626373627
Self Consistency Ratio	2.9782608695652173	3.55
Reproducibility Test	borderline	borderline

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	rep4	rep5
Number of peaks	365	352	98	146	112

Top 500000 raw peaks from macs2 with p-val threshold 0.01

Peak calling statistics

Peak region size

	rep1	rep2	rep3	rep4	rep5	idr_opt	overlap_opt
Min size	150.0	150.0	151.0	150.0	150.0	154.0	154.0
25 percentile	195.0	195.0	214.5	219.5	208.5	234.75	219.0
50 percentile (median)	258.0	266.0	255.5	275.5	252.5	277.5	271.0
75 percentile	431.0	429.0	315.0	346.0	311.25	338.0	329.0
Max size	1203.0	1474.0	610.0	934.0	617.0	926.0	926.0
Mean	330.2520547945206	337.4119318181818	275.234693877551	295.8904109589041	271.25892857142856	302.88709677419354	290.6350364963504

Enrichment / Signal-to-noise ratio

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

	rep1	rep2	rep3	rep4	rep5
Number of Subsampled Reads	1410390	2041921	3553123	5196510	7686615
Estimated Fragment Length	100	125	95	60	105
Cross-correlation at Estimated Fragment Length	0.236993000623076	0.249853308956774	0.762524155856539	0.726235716996382	0.843105972022676
Phantom Peak	45	40	45	40	45
Cross-correlation at Phantom Peak	0.2307862	0.2431638	0.7630505	0.7264739	0.8450074
Argmin of Cross-correlation	1500	1500	1500	1500	1500
Minimum of Cross-correlation	0.1974579	0.211017	0.7548264	0.7143706	0.8350714
NSC (Normalized Strand Cross-correlation coeff.)	1.200221	1.184043	1.010198	1.016609	1.009621
RSC (Relative Strand Cross-correlation coeff.)	1.186233	1.208095	0.9360014	0.980317	0.8086302

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

Jensen-Shannon distance (filtered/deduped BAM)

	rep1	rep2	rep3	rep4	rep5
AUC	0.30423629433136185	0.3083218026096779	0.4039898621420047	0.3927340898095576	0.40752912564282007
Synthetic AUC	0.49401387469891916	0.4946783906762743	0.49754634358978206	0.49744892897840604	0.4982720513644861
X-intercept	0.03896141351258371	0.03641109204435664	0.028078256552451542	0.027569428278903817	0.02702145936892934
Synthetic X-intercept	2.714371141815878e-239	2.957452334001288e-303	0.0	0.0	0.0
Elbow Point	0.6531913008905524	0.6652630971779601	0.487082559962425	0.5391705069124424	0.47596043911674
Synthetic Elbow Point	0.5004316649607212	0.5076828396304471	0.5017343551607188	0.503054371865085	0.49960339524452335
JS Distance	0.12682669122131754	0.12879067245284692	0.1565582177945924	0.14387462137561702	0.1626937897804811
Synthetic JS Distance	0.2912705153795955	0.2885511642693098	0.15401066564274682	0.17428623664107276	0.15756260336371408
% Genome Enriched	34.28946354667727	32.65791701773071	54.830881550134	47.9163791203245	60.843707318681
Diff. Enrichment	19.93219845240462	19.632469158425884	7.17607401954361	7.740560012720738	5.521200429133765
CHANCE Divergence	0.1698701352007036	0.16735512782470122	0.06341552266273362	0.06659756841105843	0.05107797860642931

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for macs2 raw peaks

	rep1	rep2	rep3	rep4	rep5	rep1-pr1	rep2-pr1	rep3-pr1	rep4-pr1	rep5-pr1	rep1-pr2	rep2-pr2	rep3-pr2	rep4-pr2	rep5-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.12561217540638972	0.12400303125277748	0.019841679795449263	0.034397744184897806	0.023437811447231456	0.13566378074923313	0.13575083967180293	0.020300111056587206	0.03511825633911103	0.02388025470434275	0.13920669888194048	0.1342785771756825	0.02044812028282676	0.033887694597340014	0.023671600772500252	0.031988009536678005	0.032253469415700814	0.03208050810852539

FRiP for overlap peaks

	rep1_vs_rep2	rep1_vs_rep3	rep1_vs_rep4	rep1_vs_rep5	rep2_vs_rep3	rep2_vs_rep4	rep2_vs_rep5	rep3_vs_rep4	rep3_vs_rep5	rep4_vs_rep5	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	rep3-pr1_vs_rep3-pr2	rep4-pr1_vs_rep4-pr2	rep5-pr1_vs_rep5-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.031988009536678005	0.027906753400778733	0.031504260005665766	0.029285973744956586	0.027906753400778733	0.031504260005665766	0.029285973744956586	0.027906753400778733	0.027202438897184326	0.029285973744956586	0.11448198264886152	0.1166354029741829	0.01936238817356615	0.03302920060733484	0.023009383097628018	0.031641079215220635

FRiP for IDR peaks

	rep1_vs_rep2	rep1_vs_rep3	rep1_vs_rep4	rep1_vs_rep5	rep2_vs_rep3	rep2_vs_rep4	rep2_vs_rep5	rep3_vs_rep4	rep3_vs_rep5	rep4_vs_rep5	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	rep3-pr1_vs_rep3-pr2	rep4-pr1_vs_rep4-pr2	rep5-pr1_vs_rep5-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.027536617806164284	0.025072493503097905	0.02694005848188346	0.024371625327200094	0.023464092367096394	0.030999947386063834	0.024488570713704597	0.022346218539910426	0.02177631081648328	0.025155550000585877	0.09753649364877269	0.09364138595613104	0.012618531549805601	0.02721409841487326	0.021423386134276974	0.027225414415161638

For macs2 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