Bioinformatics Forum

RNA-Seq output files

What are the output files from the RNA-Seq pipeline?

Gilgi Friedlander
1 Answer

Hi Gilgi,

The RNA-Seq pipeline has several output files, all written into the project and run directories:

  • Mapping is run once per project therefore the mapping results are saved under mapping directory at the top level of the project directory.
  • Counts results are saved in the run folder under counts
  • DESeq2 results are saved in the run folder under differential_expression directory
  • QA of the samples, under analysis folder, including the following plots:
      1. Hierarchical clustering of the samples
      2. PCA
      3. Cluster heatmap
      4. File for each sample with a pie chart showing gene count distribution

Nofar Chen

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