COV434_DOXY

COV434_DOXY json file for ATAC

Pipeline version: v1.4.2

Report generated at 2019-08-16 23:08:25

Paired-end: [True]

Pipeline type: ATAC-Seq

Genome: hg19.tsv

Peak caller: MACS2

Alignment


Marking duplicates (filtered BAM)

Filtered out (samtools view -F 1804):


rep1 (PE)
Unpaired Reads0
Paired Reads112474184
Unmapped Reads0
Unpaired Dupes0
Paired Dupes33212948
Paired Opt. Dupes1254856
% Dupes/1000.2953

Library complexity (filtered non-mito BAM)

rep1 (PE)
Total Reads (Pairs)104141571
Distinct Reads (Pairs)79052163
One Read (Pair)60258543
Two Reads (Pairs)14176744
NRF = Distinct/Total0.7591
PBC1 = OnePair/Distinct0.7623
PBC2 = OnePair/TwoPair4.2505

Mitochondrial reads are filtered out.

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally


Flagstat (filtered/deduped BAM)

Filtered and duplicates removed

rep1 (PE)
Total158522472
Total(QC-failed)0
Dupes0
Dupes(QC-failed)0
Mapped158522472
Mapped(QC-failed)0
% Mapped100.0000
Paired158522472
Paired(QC-failed)0
Read179261236
Read1(QC-failed)0
Read279261236
Read2(QC-failed)0
Properly Paired158522472
Properly Paired(QC-failed)0
% Properly Paired100.0000
With itself158522472
With itself(QC-failed)0
Singletons0
Singletons(QC-failed)0
% Singleton0.0000
Diff. Chroms0
Diff. Chroms (QC-failed)0

Peak calling


IDR (Irreproducible Discovery Rate) plots

rep1-pr
rep1-pr

Reproducibility QC and peak detection statistics

The number of peaks is capped at 300K for peak-caller MACS2


overlapIDR
Nt00
N1213158135186
Np00
N optimal213158135186
N conservative213158135186
Optimal Setrep1-prrep1-pr
Conservative Setrep1-prrep1-pr
Rescue Ratio0.00000.0000
Self Consistency Ratio1.00001.0000
Reproducibilitypasspass

Overlapping peaks


IDR (Irreproducible Discovery Rate) peaks


Enrichment


Strand cross-correlation measures

Performed on subsampled reads (25M)

rep1
Reads25000000
Est. Fragment Len.0
Corr. Est. Fragment Len.0.3619
Phantom Peak150
Corr. Phantom Peak0.2854
Argmin. Corr.1500
Min. Corr.0.2271
NSC1.5933
RSC2.3134

NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.


rep1
rep1

Fraction of reads in overlapping peaks

rep1-pr
Fraction of Reads in Peak0.2501


Fraction of reads in IDR peaks

rep1-pr
Fraction of Reads in Peak0.2151


ATAQC


Summary table

rep1
Genomemale.hg19.fa.gz
Paired/single-endedPaired-ended
Read lengthN/A
Read count from sequencer275072572
Read count successfully aligned273905197
Read count after filtering for mapping quality226836091
Read count after removing duplicate reads193623143
Read count after removing mitochondrial reads (final read count)158522472
Mapping quality > q30 (out of total)226836091, 0.824640891495
Duplicates (after filtering)33212948, 0.295294
Mitochondrial reads (out of total)31660220, 0.115588241285
Duplicates that are mitochondrial (out of all dups)14732128, 0.221782902258
Final reads (after all filters)158522472, 0.576293269981
NRF = Distinct/Total0.759084, out of range [0.8, inf]
PBC1 = OnePair/Distinct0.762263, out of range [0.8, inf]
PBC2 = OnePair/TwoPair4.250521, OK
Picard est library size185978300
Fraction of reads in nfr0.223780123322, out of range [0.4, inf]
Nfr / mono-nuc reads0.528581053485, out of range [2.5, inf]
Presence of nfr peakOK
Presence of mono-nuc peakOK
Presence of di-nuc peakOK
Naive overlap peaks213158, OK
Idr peaks135186, OK
Naive peak stats: min size150.0000
Naive peak stats: 25 percentile511.0000
Naive peak stats: 50 percentile (median)791.0000
Naive peak stats: 75 percentile1183.0000
Naive peak stats: max size3671.0000
Naive peak stats: mean894.0926
Idr peak stats: min size150.0000
Idr peak stats: 25 percentile656.0000
Idr peak stats: 50 percentile (median)977.0000
Idr peak stats: 75 percentile1373.0000
Idr peak stats: max size3671.0000
Idr peak stats: mean1052.3530
Fraction of reads in universal dhs regions51731104, 0.330361522487
Fraction of reads in blacklist regions252868, 0.001614847761
Fraction of reads in promoter regions25173240, 0.160759567249
Fraction of reads in enhancer regions43556488, 0.278157367179
Fraction of reads in called peak regions33684563, 0.215113977019

Replicate 1

Sample Information

Sample
Genome male.hg19.fa.gz
Paired/Single-ended Paired-ended
Read length N/A

Summary

Read count from sequencer 275,072,572
Read count successfully aligned 273,905,197
Read count after filtering for mapping quality 226,836,091
Read count after removing duplicate reads 193,623,143
Read count after removing mitochondrial reads (final read count) 158,522,472
Note that all these read counts are determined using 'samtools view' - as such,
these are all reads found in the file, whether one end of a pair or a single
end read. In other words, if your file is paired end, then you should divide
these counts by two. Each step follows the previous step; for example, the
duplicate reads were removed after reads were removed for low mapping quality.
This bar chart also shows the filtering process and where the reads were lost
over the process. Note that each step is sequential - as such, there may
have been more mitochondrial reads which were already filtered because of
high duplication or low mapping quality. Note that all these read counts are
determined using 'samtools view' - as such, these are all reads found in
the file, whether one end of a pair or a single end read. In other words,
if your file is paired end, then you should divide these counts by two.

Filtering statistics

Mapping quality > q30 (out of total) 226,836,091 0.825
Duplicates (after filtering) 33,212,948 0.295
Mitochondrial reads (out of total) 31,660,220 0.116
Duplicates that are mitochondrial (out of all dups) 14,732,128 0.222
Final reads (after all filters) 158,522,472 0.576
Mapping quality refers to the quality of the read being aligned to that
particular location in the genome. A standard quality score is > 30.
Duplications are often due to PCR duplication rather than two unique reads
mapping to the same location. High duplication is an indication of poor
libraries. Mitochondrial reads are often high in chromatin accessibility
assays because the mitochondrial genome is very open. A high mitochondrial
fraction is an indication of poor libraries. Based on prior experience, a
final read fraction above 0.70 is a good library.
  

Library complexity statistics

ENCODE library complexity metrics

Metric Result
NRF 0.759084 out of range [0.8, inf]
PBC1 0.762263 out of range [0.8, inf]
PBC2 4.250521 - OK
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.

Picard EstimateLibraryComplexity

185,978,300

Yield prediction

Preseq performs a yield prediction by subsampling the reads, calculating the
number of distinct reads, and then extrapolating out to see where the
expected number of distinct reads no longer increases. The confidence interval
gives a gauge as to the validity of the yield predictions.

Fragment length statistics

Metric Result
Fraction of reads in NFR 0.223780123322 out of range [0.4, inf]
NFR / mono-nuc reads 0.528581053485 out of range [2.5, inf]
Presence of NFR peak OK
Presence of Mono-Nuc peak OK
Presence of Di-Nuc peak OK
Open chromatin assays show distinct fragment length enrichments, as the cut
sites are only in open chromatin and not in nucleosomes. As such, peaks
representing different n-nucleosomal (ex mono-nucleosomal, di-nucleosomal)
fragment lengths will arise. Good libraries will show these peaks in a
fragment length distribution and will show specific peak ratios.

Peak statistics

Metric Result
Naive overlap peaks 213158 - OK
IDR peaks 135186 - OK

Naive overlap peak file statistics

Min size 150.0
25 percentile 511.0
50 percentile (median) 791.0
75 percentile 1183.0
Max size 3671.0
Mean 894.092560448

IDR peak file statistics

Min size 150.0
25 percentile 656.0
50 percentile (median) 977.0
75 percentile 1373.0
Max size 3671.0
Mean 1052.35303952
For a good ATAC-seq experiment in human, you expect to get 100k-200k peaks
for a specific cell type.

Annotation-based quality metrics

Annotated genomic region enrichments

Fraction of reads in universal DHS regions 51,731,104 0.330
Fraction of reads in blacklist regions 252,868 0.002
Fraction of reads in promoter regions 25,173,240 0.161
Fraction of reads in enhancer regions 43,556,488 0.278
Fraction of reads in called peak regions 33,684,563 0.215
Signal to noise can be assessed by considering whether reads are falling into
known open regions (such as DHS regions) or not. A high fraction of reads
should fall into the universal (across cell type) DHS set. A small fraction
should fall into the blacklist regions. A high set (though not all) should
fall into the promoter regions. A high set (though not all) should fall into
the enhancer regions. The promoter regions should not take up all reads, as
it is known that there is a bias for promoters in open chromatin assays.

Comparison to Roadmap DNase

This bar chart shows the correlation between the Roadmap DNase samples to
your sample, when the signal in the universal DNase peak region sets are
compared. The closer the sample is in signal distribution in the regions
to your sample, the higher the correlation.