Standard bioinformatic analysis

Each sample operated onto the platform with standard protocols, including RNA-seq, smallRNA-seq, ChIP-seq, DNA-seq, ClIP-seq is necessary charge 50€ for academics and 100€ for private companies for the bioinformatics primary analysis including:

• Production of raw data .FASTQ files for each library,
• Provision of a standardized run info file for raw data quality assessment,
• Storage of ordering information and wet lab experiment quality controls within Mediante web server,
• Backup of raw data onto USB disks for the next 6 months after experiment is delivered,
• Support for GEO submission of your NGS experiment within the next 12 month

We also provide a second level of bioinformatics support including the secondary and tertiary/statistical analysis that is charged 50€ for academics and 100€ for private companies. This step of the bioinformatics analysis require a close collaboration and close discussion with the project carrier. The different steps of the analysis has to be discussed during a pre-experiment meeting or a phone call in order to define the biologically relevant questions that should be answered by the experiment and the bioinformatics analysis. This package include :

• FastQC analysis of raw reads for quality assessment dor DNA samples,
• Mapping to required genome build with latest and most accurate aligners (STAR, Hisat, Bowtie2),
• In case of RNA-seq and smallRNA-seq, production of count table for following statistical analysis,
• In case of DNA-seq SNPs calling .vcf files obtains with GATK or Isaac will be provided,
• In case of ChIP-seq, peaks calling files obtains with Homer or Macs2 will be provided,
• A custom statistical analysis will also be provided for counting experiment (RNAS-seq, smallRNA-seq),
• IPA functional analysis can also be provided.

Concerning the Single Cell projects actually performed on the 10xGenomics Chromium system available at UCAGenomiX we define a standard fee for bioinformatics analysis of 460€. It includes the setup of a standardized analysis using 10x Genomics CellRanger software pipeline. We offer the possibility to collaborate and to perform a limited number of custom ad'hoc analysis within Seurat R package suite.

All analyses are loaded and provided through our secure Mediante web server.