With the large production of data generated by high throughput experiments, the iBV has recently engaged in the creation of a bioinformatics core facility. The primary goal is to provide all iBV researchers a local expertise and technology platform for their needs related to bioinformatics, biostatistics, data storage etc. Due to an already existing and an expected increase of the demand for next generation sequencing data analysis the first priority was given to the setup of a local instance of a GALAXY web platform. The iBV has purchased a dedicated server and installed all the softwares required for processing and analysis of Chip-seq and RNA-seq data using GALAXY. Additional tools are also available for pathway and network analysis using CYTOSCAPE and INGENUITY. Researchers will also benefit from assistance for the design and statistical analysis of their NGS experiments. Besides regular service, the platform also develops collaborative projects with research teams that are addressing unconventional issues.
RNA-seq and Chip-seq: a complete workflow is available on our Galaxy server from sequences (fastq file) to the final result table with protein binding site peaks or differentially expressed genes. The advice workflow for Chip-seq is first checking the sequences with FAstQC following by mapping with Bowtie2 and peak calling with MACS. For RNA-seq, after checking the sequence with FastQC, alignment is done with Tophat, the count matrix build with HTseq and finally the differential count done with edgeR and DESeq.
For people who needs some extra analysis, the facility can install packages and help them to use the software.
Pathway analysis: The main tool used to this expertise are IPA (Ingenuity Pathway Analysis). It is one of the leading tools for biologists allowing to model and analyze complex omics data. Cytoscape is another very useful free software used. It allows using data available on the network such as WikiPathways, Reactome, Kegg, BioGrid…and to build, analyze and construct networks from omics data.
The facility has expertise in using many free access tools through the web. Some of these websites are for motif analysis (http://meme-suite.org/, http://bejerano.stanford.edu/great/public/html/), ontology (http://geneontology.org/, http://biit.cs.ut.ee/gprofiler/index.cgi, https://david-d.ncifcrf.gov/), pathway analysis (http://www.webgestalt.org/login.php, https://toppgene.cchmc.org/), genome browser (http://genome-euro.ucsc.edu) or data searching (http://www.pathguide.org/, http://www.ebi.ac.uk/arrayexpress/ ).
An expertise in R software is also provided, all basic commands to manipulate table, plot data, are used as well as basic statistic and some useful packages like gPower, FactoMineR. This also includes running Bioconductor packages when the software or option are not available in Galaxy.
iBV has his own Galaxy web server. It allow to perform sequence analysis in a user friendly way. A Dell PowerEdge R920 server is dedicated for computing with Galaxy, it’s main characteristics are 4 processors 12 cores, 512 Go RAM, 1.8 To in 2 internal drives, 4 additional 1To drives is planned in a near future to extend temporary storage capacity. An additional 600 Go is available on a secured computer for data storage.
A virtual computer for IPA and Cytoscape analysis allows all the iBV staff to access easily to these tools for network analysis.
The facility uses many free access website for different purpose.
iBV - Institut de Biologie Valrose
"Centre de Biochimie"
Université Nice Sophia Antipolis
Faculté des Sciences
06108 Nice cedex 2