Nucleosee

Nucleosome is web-based nucleosome map visual browser backed up by BWT-based pattern searches. It can be used for other kinds of high-throughput genomic data as well.

Working example

If you want to give it a quick look there is a server set up for tests at http://cpg3.der.usal.es/nucleosee Try loading samples 972h and Dhta1 and perform some analyses as explained in this video: http://cpg3.der.usal.es/nucleosee/nucleosee.mp4

Help

For further help please check http://cpg3.der.usal.es/nucleosee/help.pdf

Install

If you want to install your own Nucleosee server, it is available as an Nginx Docker container at efialto/nucleosee in the Docker repository. This is a stable version ready to run, which may not correspond to the latest code in the GitHub repository, if you want to build a fully updated container you have the components -Dockerfile, etc.- in the repository.

You basically need to perform 3 steps:

1) Install Docker

Visit https://docs.docker.com/install/ to install Docker on your machine, if you haven't it already installed.

2) Setup host folders

This step is optional, as long as you provide two folders with the proper structure for volumes (-v) in the next step, it's fine. More info about it in the help pdf above (section Setting up a server).

Anyways, we recommend to do it at least the first time you're setting up Nucleosee.

Download the annotations folder at http://vis.usal.es/rodrigo/nucleosee/annotations.zip

Unzip it at your preferred location (ann_path). You can check its folder structure and add your own organism annotations.

Download some preprocessed examples at http://vis.usal.es/rodrigo/nucleosee/genomes.zip

Unzip it at your preferred location (gen_path)

3) Run Docker container

docker run -it --rm -p 80:80 -v ann_path:/app/annotations -v gen_path:/app/genomes -e SERVERNAME=server_name efialto/nucleosee

gen_path and ann_path relate to the folders created in step 2. server_name must be the name of the machine were you're setting up the server (e.g. signus.opus.uk)

Contact

If you have any doubts about the code or the install, you can write to rodri AT usal DOT es

Citation

For more detailed info please check our paper and cite us if you find it useful!

Santamaría, R., Therón, R., Durán, L., García, A., González, S., Sánchez, M., & Antequera, F. (2019). Genome-wide search of nucleosome patterns using visual analytics. Bioinformatics, 35(13), 2185-2192 https://academic.oup.com/bioinformatics/article/35/13/2185/5216313