COV2HTML provides an easy and 'in home' web interface for biologists that allows coverage visualization of the NGS alignment needed for the analysis. It combines two essential processes: (i) MAP2COV, a tool that converts the huge NGS mapping or coverage files into light specific coverage files which contains genetic elements informations. (ii) COV2HTML, a visualization interface allowing a real-time analysis of data with selected criteria. Thus this interface offers a visualization of NGS mapping coverage data (DNA-seq, RNA-seq, ChIP-seq and TSS) performed in different prokaryotic organisms (bacteria, viruses...) or different experimental conditions (mutant versus wild type strains or different growth states…) facilitating studies.

Features

  • RNA-Seq strand coverage visualization : Black (strand +), Purple (strand -)
  • ncRNA feature analysis
  • X and Y Zooms are supported
  • Security enhanced: HTTPS as default

Project Samples

MAP2COV Tcl/Tk graphical interface. Three parts must be filled out (i) Reference information: GenBank, EMBL file or Genome and Annotation files; (ii) Alignment File: SAM/BAM, Eland or Wig files; Data type: DNA, RNA, TSS or ChIP; (iii) Optional Parameters: Anonymize, Read-length, Strand-specific or Genetic Elements Coverage Style. COV2HTML connexion.php web page. a) An analysis is specified by a title, a label attached to condition A and B (optional), up to 8 files using the “Choose File” button and a statistical results file (optional). To enter analysis in database press the action button. b) Analyses stored in database. YOUR Analysis (User’s analysis), TUTORIAL Data and a Remove Analysis button. COV2HTML visualization.php web page. We divided the webpage into color boxes to separate each part. [Grey box] Analysis title and strand. [Orange box] information of Gene or IGR: gene ID or IGR ID; position; strand; type; product; coverage for each replicates; the mean value per condition; the ratio of conditions A/B. [Purple box] Navigation tools within genome. Current gene or IGR surround with link to the previous and next one. A Y-axis button to change coverage scale from 1-250 to 1-2500. [Blue box] Genetic elements in genomic view. Gene in blue, rRNA and tRNA are in red. [Yellow box] Sample’s coverage: analysis condition and replicate genomic coverage views. One graphical bar (one pixel) represents a genomic base coverage. [Green box] Gene or IGR filters to analyse coverage data. At the top others tools : search for a position or a gene ID; activate help boxes; export all or filtered results in a comma-separated value file (Excel compatible). To demonstrate the relevance of COV2HTML, the program was tested with NGS data from a Campylobacter jejuni RNA-seq article, which presents a standard comparison of 2 experimental conditions (wild-type and mutant) with 2 replicates. COV2HTML combine analysis. Three coverages from two experiments done with the same genome reference, RNA-seq and TSS, were mixed in one view. a) Strand plus transcriptional start site (TSS+); b) non-stranded RNA-seq, to detect gene expression; c) Strand minus transcriptional start site (TSS-). A dashed red insert show the 10x Y-scale zoom of TSS region. In TSS experiments green lines represent the first base coverage of sequence reads. COV2HTML Genetic elements filter box. Example of a two-conditions RNA-seq experiment without statistics. From top to bottom: Experiment type selection switch between Genes, ncRNA and IGR analysis; Standardization ON/OFF: Switch button to equilibrate the mean coverage of each sample (figure 5A); The blue rectangle represents the one condition panel: Filter genetic elements by their coverage. The red rectangle represents the two condition comparison panels: Filter fold change differences by setting the minimum coverage value assigned to genetic elements before ratio calculation (threshold); Results are displayed below the filter box (Figure 3). If statistical results are present, ‘Standardization’ is replace by ‘Statistics’ and ‘threshold’ option disapears.

Project Activity

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Categories

Data Visualization

License

GNU General Public License version 3.0 (GPLv3)

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Additional Project Details

Operating Systems

Linux, Mac, Windows

Intended Audience

Science/Research

User Interface

Project is a user interface (UI) system, Tk

Programming Language

PHP, Python

Database Environment

MySQL

Related Categories

Python Data Visualization Software, PHP Data Visualization Software

Registered

2012-04-24
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