ViewR

ViewR is a web browser based tool for NGS data exploration.
It displays images of read coverage across the genome from any "omic" data (RNA-seq, ChIP-seq, etc), along with the corresponding gene annotation.

How It Works

All the data are on the server side. It takes coverage data as bigWig files and annotation as gtf file. It runs with Apache on Ubuntu, and requires php and python3, with pyBigWig and pytabix libraries. It makes also use of the Plotly graphical library.

Browser Compatibilities

Chrome	Firefox
✔	✔

Installation

1. Clone the repository

git clone https://github.com/szachn-u/ViewR.git

2. Edit description file

Edit description.tsv, a tab separated file, with header, one sample per line:

• file_F : name of the bigWig file for the reads from the forward strand (or all reads, if the library is unstranded, e.g. like ChIP-seq).
• file_R : name of the bigWig file for the reads from the reverse strand (for strand-specific libraries only).
• replicate_name : short name for the sample.
• cond_name : condition of the sample.
• norm_coeff : normalisation factor. The coverage will be multiplied by this value if normalized data are asked.

3. Run config.sh script

cd ViewR
# requires bedtools and htslib to be installed
./conf.sh --description /path/to/description.tsv --bw_dir /path/to/bw_files --annot my_annot.gtf --genome_info genome_info.tsv --out_dir /path/to/myViewR --python_path /path/to/python

• description.tsv, the file edited previously
• bw_dir, the directory where are stored the bigWig files
• my_annot.gtf, gene annotation file, should be in gtf format, with gene_id, gene_type and gene_name in the attribute column (9th)
• genome_info.tsv, a tab separated file, without header, with chromosome names (as in bigWig files) and chromosome sizes
• /path/to/myViewR, the directory to store your ViewR files
• /path/to/python, refers to your python path, with pybigWig and pytabix installed

4. Copy the output of ./conf.sh on the server

sudo cp -r /path/to/myViewR/ /var/www/html/
sudo chmod -R +x /var/www/html/myViewR   # to allow execution of the scripts

5. Launch ViewR

You can access your ViewR by typing localhost/myViewR in the adress bar of your web browser

Authors

Ugo Szachnowski [email protected]