Standard bioinformatic analysis

  Académique Privé
Primary analysis, Mediante storage and .fastq production (per sample) 50 100
Up-to-date secondary and tertiary analysis (per sample) 50 100
Low input and Single Cell projects (C1 96 cells, 24 low-input samples) 340 680

 

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 Fluidigm C1 system available at IPMC, and the Low Input projects (i.e. samples with less than 100 cells), we define a standard fee for bioinformatics analysis of 340€. It includes the analysis for one C1 plate (96 single cells) and for Low Input projects with less than 24samples. Concerning analysis of Fluidigm C1 HT chip (800 cells), 2 x 340€ will be charged. The Single cell analysis package include :

  • Globals statistics of samples (number of reads produced, mapped and counted, ...)
  • QC of samples and protocol including capture efficiency with ERCC spike-ins,
  • Production of raw count based on Unique Molecular Identifiers,
  • Cell-2-cell correlation, PCA and clustering analysis

 

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