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Cambridge Genomic Services

A Next-Generation Sequencing and Array Facility in the Department of Pathology

Studying at Cambridge

 

Automated Pipelines

Our automated pipelines are designed for standard projects, for which the experimental design is common and relatively simple. For example a standard RNA-Seq or methylation experiment would be to compare two groups to generate a list of differentially expressed genes or methylated loci.  

The pipelines were designed following best practices in accordance with the type of analysis. Depending on the application different tools will be used, all the tools used and their version are referenced in the analysis report. 

An hour consultation or phone call to discuss the report and results can be requested.


Briefly the analysis is as follows:

 

Next-Generation Sequencing Analysis Automated Pipeline

  • Pre-processing of the reads: trimming of the reads, QC pre- and post-trimming 

  • Mapping of the reads 

  • Mapping QC 

  • Read count / methylation extraction / peak calling / variant calling (depending on the application)

  • Comparisons between groups 
  • Report generation 

 

Microarray Analysis Automated Pipeline

  • Technical and sample QC 

  • Data normalisation / Genotype calling (depending on the application)

  • Post normalisation QC 

  • Comparison between groups 

  • Report generation