Nucleic Acid Viewer beta

NAVi

Text search

Search thousands of experiments by organism, technique, biological source, author…

Search
  • Search queries are case insensitive.
  • Enclose a group of words in double quotes to search for an exact phrase (e.g. "embryonic stem cell").
  • Use the plus sign (+) to combine several independent searches (e.g. Human H3K4me3 MCF-7 + Human Cebpb K-562).
  • Filter by quality (e.g. AAA) or by a range of quality (e.g. "A-C" to retrieve datasets having a quality between AAA and CCC).
Results
  • Click on a row to select/unselect the experiment. Selected experiments are highlighted in green.
  • Click the button to display more information.
Displaying results 0 - 0 of 0  Quality chart
Accession Organism Sample Experiment Mapped Reads QC stamp
No entries found

Chromatin interactions

Browse over hundred of publicly available 3D experiments such as Hi-C.

Search
  • Search queries are case insensitive.
  • Enclose a group of words in double quotes to search for an exact phrase (e.g. "Mus musculus").
Results
  • Click on a row to select/unselect the experiment. Selected experiments are highlighted in green.
  • Click the button to display more information.

Displaying results 0 - 0 of 0
Accession Organism Sample Experiment Intra PETs
No entries found

Genome browser

Visualize enrichment sites, read coverage, and chromatin organization in one place with our lightweight genome browser.

Enter a gene symbol or genomic coordinates, then click the Browse button to start exploring. Right-click on a track to display more information, update settings, etc.

Custom tracks

Add custom tracks to visualize your data along publicly available experiments.

Supported data:
  • Genome coverage (i.e. read count per fixed-size genomic window) in the bigWig format.
  • Hi-C contact maps, stored in the hic format.
For more information, please refer to the documentation.

Name Type Genome
No tracks added

Documentation

This manual presents NAVi, describes how to use the web application, and illustrates features with examples. We recommend that you read it carefully, and refer to it for future reference.

Last updated: 13 September 2017.

Getting started

NAVi is data portal allowing to search, and visualize publicly available high-throughput sequencing data sets. The raw data were collected from public repositories, uniformly processed, and annotated using controlled vocabularies.

Accessing QC Genomics

QC Genomics is available online at http://ngs-qc.org/qcgenomics. Alternatively, NAVi can be directly accessed at http://ngs-qc.org/navi.

Overall look

A tour presenting the search and visualization features can be started by clicking the "Start the tour" button on the main portal or by clicking the following link: take the tour.

Portal

Text search
Find experiments integrated in the NGS-QC database using complex search queries.

Genome interactions
List Hi-C, and other chromatin structure experiments from the LOGIQA collection.

Data visualization
Explore experiments of interest with our lightweight genome browser.

User-submitted data
Visualize your data, and compare them to publicly available data sets.

Find relevant *Seq experiments by using the Search and Chromatin interactions to search the NGS-QC (ChIP-seq, DNAse-seq, etc.) and LOGIQA (Hi-C, ChIA-PET, etc.) databases, respectively.

2D experiments

The video below shows how to search for H3K27ac and FAIRE-seq data, then order, filter, and select experiments of interest.

H3K27ac is an epigenetic mark associated with active promoters and enhancers, and FAIRE-seq is a method for identifying open chromatin regions.

Supported search terms
Organism
Scientific name (e.g. Homo sapiens), common name (e.g. human) or genome assembly (e.g. hg19).
See the supported organisms for more information.
Experiment
Method or protocol (e.g. DNAse-seq), or a transcription factor or histone mark for ChIP-seq data. For most transcription factors, the same results are returned whether you enter an official identifier (e.g. SOX9) or an alias (e.g. CMPD1).
Sample
Biological source: tissue, cell type, or cell line.
Accession
GEO identifier (e.g. GSM1239499) or PubMed identifier (e.g. 23953112) if the experiment is part of a publication referenced in PubMed.
Author
Not necessary the first author: for each publication, all authors are stored in our database (e.g. Kellis).
Abstract
Any keyword from a publication's abstract (e.g. "Breast cancer").
Quality stamp
By evaluating the effect of random sampling on a given profile, NGS-QC Generator infers a quality score represented by a triple letter rating: from best (AAA) to worst (DDD). Unfortunately, sometimes there are too few data sets with an AAA quality. If so, you can extend the search to BBB quality data sets by searching A-B to retain all data sets having a quality between AAA and BBB.
Searching method
Case insensitive
Searching Human H3K4me3 or hUMaN h3k4ME3 returns the same results.
Phrase search
In order to search for an exact group of words, surround them by double quotes (e.g. "embryonic stem cell").
Grouping
Searching Human Cebpb H3K9ac returns human ChIP-seq experiments for the Cebpb transcription factor, and the (human) experiments for the H3K9ac mark.
A more complex example is Human H3K4me3 MCF-7 Cebpb K-562. As of June 2017, this query returns 116 entries:
  • 88 entries for H3K4me3 in the K-562 cell line
  • 4 entries for Cebpb in the K-562 cell line
  • 22 entry for H3K4me3 in the MCF-7 cell line
  • 2 entry for Cebpb in the MCF-7 cell line
To retrieve H3K4me3 MCF-7 and Cebpb K-562 experiments only, use the plus sign ('+') as follows: Human H3K4me3 MCF-7 + Human Cebpb K-562.

3D experiments

The integration and visualization of Hi-C data with other genomic data remains a challenge because of its complexity. Several tools to visualize Hi-C data have already been described, and some include publicly available data sets. However, NAVi is the only application that comes with thousands of data sets.

Open the Chromatin interactions panel, to search chromosome conformation capture data sets. The search principles are the same than for 2D experiments.

Data visualization

Please note that it is not possible to simultaneously visualize data from different organisms. If you open the Genome browser tab having selected experiments from more than one organism (e.g. Human and mouse), an error message will invite you to refine your selection.

To visualize selected experiments, open the Genome browser tab, and define a genomic region to display by entering a gene symbol or genomic coordinates. The following video shows how to integrate several experiments for visual exploration, and how to change some track settings.

The data sets used as examples in this section are listed below.

Organism Sample Experiment Source
Homo sapiens MCF-7 POL2RA ChIA-PET Li GL, et al. Cell. 2012
FOXA1 ChIP-seq Theodorou V, et al. Genome Res. 2013
RNAPol2 ChIP-seq wa Maina C, et al. PLoS Comput Biol. 2014
H3K4me3 ChIP-seq Yamamoto S, et al. Cancer Cell. 2014
H3K9ac ChIP-seq Grimmer MR, et al. Nucleic Acids Res. 2014
FAIRE-seq Hardy K, et al. Nucleus. 2016
H3K27ac ChIP-seq Rhie SK, et al. Epigenetics Chromatin. 2016
HindIII Hi-C Barutcu AR, et al. Genome Biol. 2015
MCF-10A HindIII Hi-C
GM12878 HindIII Capture Hi-C Cairns JC, et al. Genome Biol. 2016

Track types

Gene annotations

Gene annotations display genes at their respective position on the genome. The gene's sense strand is represented by less-than (<, minus strand) and greater-than (>, plus strand) symbols.

When zooming out, genes too small compared to the genomic region are not displayed. The figure below shows a zoomed out region of the previous figure: smallest genes are not represented anymore (e.g. HOXA7).

δRCI heatmap

NGS-QC Generator infers local quality indicators by evaluating the influence of random sampling on a given profile. Briefly, the genome is divided into defined windows of 500bp (referred as bins) and mapped reads are assigned to bins. Three random samplings are realised by retaining 90%, 70%, and 50% of the original reads, then the read count dispersion (δRCI) is calculated for each bin, where the dispersion represents the difference between the expected count and the observed one, expressed as a percentage. Bins with a dispersion lower than 10% for each sampling are retained.

This test is performed five times, to ensure its reproducibility. Finally, bins that have been retained at least N times (1 ≥N ≥ 5) are represented on a heatmap.

It is possible to increase or decrease N to change the stringency of the filtering (e.g. setting N = 5 shows only bins with a very strong signal).

Genome coverage

Genome coverage tracks represent signal data by calculating the read coverage that is the number of reads per bin, where bins are consecutive, fixed-size windows.

Coverage tracks are available for all 2D experiments from the NGS-QC collection. When visualizing a profile, only the δRCI heatmap is displayed by default. To load the genome coverage, right-click on the δRCI track, then select Coverage.

The scale of the Y-axis is defined according to be the greatest value within the displayed genomic region. If this value is particularly high, the rest of the signal might look like background. In order to better distinguish the profile, you can change the Y-axis maximum value by following these steps:

  1. Right-click on the coverage track
  2. select Configure
  3. change the Y-axis scale mode from Automatic to Fixed
  4. enter the desired value in the text field
  5. click Apply or Apply to all to apply the Y-axis scale limit to the current track, or to all coverage tracks, respectively.

When analysing ChIP-seq, FAIRE-seq, and enrichment related assays, it is common to consider duplicate reads as PCR duplicates and remove them, as they could contribute to false positives during peak detection. However, comparing a profile with and without duplicates can help to evaluate the library complexity. By default, coverage tracks display the signal with duplicates, but it is possible to superimpose the signal with duplicates and the signal without by following these steps:

  1. Right-click on the coverage track
  2. select Configure
  3. under Profile without PCR duplicates, check the Displayed box
  4. click Apply to refresh the track
Peaks

Peak calling is a fundamental step in the analysis of ChIP-seq and related assays data, and aims to identify protein-DNA binding events.

MACS is a popular peak caller and is particularly appropriate for transcription factor data. ChIP-seq, and chromatin accessibility experiments from the NGS-QC collection have been processed with MACS2 and the peaks called are available for visualization. To load an experiment's peaks, right-click on the δRCI track, and select Peaks in the menu (if the item is missing, it means that peaks are not yet available for this experiment).

Peaks reported by MACS2 are not filtered by p-value or q-value. However it is possible to filter those using a p-value cutoff:

  1. Right-click on the peak track
  2. select Configure
  3. enter a cutoff (e.g. 1e-30)
  4. click Apply
Genome interactions
MCF-7 chr3:58050674-69203112

Chromosome conformation capture data is represented as a heatmap where each element of the matrix corresponds to a genomic interaction, and is colored according to the contact frequency. To support zooming, four resolutions are available: 5kb, 25kb, 100kb, and 1Mb. When loading a contact map, the resolution is selected based on to the length of the current genomic region, and can be displayed by hovering the pointer over the track's name.

Flipping track
When comparing two experiments, it might be useful to have the maps facing each other. You can flip vertically a track by right-clicking it, then selecting Flip.

Changing scale
By default, the 90th percentile is used as maximum value for the heat map color scale. This value can be manually defined: right-click on a track, select Configure, change the Scale limit to Fixed, enter the new value, then click .

Heat maps are convenient to explore the overall structure of the chromatin, but they become limited for local visualization, as they display all data. NAVi offers the possibility to display genomic interactions as arcs between two loci. Moreover, it is possible to filter loops by contact frequency or to display only those having at least on end within a given interval.

Displaying loops as arcs
Right-click on a track, select Configure, change the display mode to Loops, select a resolution, define a contact count threshold and a genomic interval (optional), then click Apply.

The and buttons in the top left corner, allows you to condense and expand tracks horizontally.

You can use the buttons above the gene annotation track to navigate upstream or downstream, and to zoom in or out.

You may also navigate upstream or downstream by clicking on any track, hold, drag to the desired genomic position, then release.

To zoom in to a precise location, click on the gene track or the genome coordinate axis, hold, drag to the desired position, then release.

Sharing

A session can be shared with other investigators by saving currently visualized experiments, settings, and genomic coordinates. Click the button to generate a shareable link: anyone with this link can load the session. Shareable links last seven days.

Adding tracks

Because visual inspection of biological data is important, NAVi allows investigators to explore their data along publicly available experiments.

BigWig

The BigWig format is a binary, compressed, and indexed version of the wiggle format. It is designed to display dense, continuous data (e.g. genome coverage), and supports zooming by storing data at different resolutions.

Click here for more information on the bigWig format.

NarrowPeaks

The narrowPeak format is used to store called peaks of signal enrichment. When calling peaks with MACS2, a narrowPeak file is produced, unless the --broad flag is on.

Click here for more information on the narrowPeak format.

HiC

Please note that it is not yet possible to select a normalization.

The hic format is binary, compressed, and indexed file format designed to store Hi-C contact maps at multiple resolutions.

Click here for more information on the hic format.

Supported organisms

The table below contains the reference genomes used to process publicly available data.

Organism Common name Genome assembly
Arabidopsis thaliana Arabidopsis TAIR10
Caenorhabditis elegans Worm ce10
Danio rerio Zebrafish danRer7
Drosophila melanogaster Fruitfly dm3
Gallus gallus Chicken galGal4
Homo sapiens Human hg19
Mus musculus Mouse mm9
Pan troglodytes Chimpanzee panTro4
Rattus norvegicus Rat rn5
Saccharomyces cerevisiae Yeast sacCer3

Contributors

Matthias Blum
Data processing – NAVi development
Pierre-Etienne Cholley
Data curation and integration – Comparator/ChromStater main development
Anissa Djedid
Comparator/ChromStater additional development
Samuel Nicaise
Comparator/ChromStater additional development
Marco Antonio Mendoza-Parra, PhD
NGS-QC Generator concept and development
Hinrich Gronemeyer, PhD
Principal investigator

Overview of the experiment quality in the context of sequencing depth. The x-axis show the number of successfully mapped reads, and the y-axis shows the quality score (δRCI<10%) inferred by NGS-QC Generator.

Series

Experiment details

Experiment
Sample
Organism
Antibody
QC stamp
Mapped reads
Unique reads
Series
Publication(s)

Experiment details

Experiment
Sample
Organism
PETs
Intra PETs
Inter PETs
Publication(s)
Loading

Track details

Experiment
Sample
Antibody
QC stamp
Total mapped reads
Unique mapped reads
PETs
Intra-PETs
Inter-PETs
Accession

Track settings

LocalQC filtering

Only display bins with at least replicates having dRCI < 10%.
Applied to all tracks.

Y-axis scale
Color
Feature filtering

Enter a threshold value to filter genomic features.

Y-axis scale
Profile without PCR duplicates
Colors
Display
Loop filtering

Enter a minimal contact frequency to filter loops (min: 5).

Display loops with at least one end within a given interval.

Drop files here
Name Type Genome Progress

Share with others

Anyone with this link can view your selection in the current genomic region.