Step 3 - map gene/transcript IDs

To be able to link gene ages assignments from an orthomap and gene or transcript of scRNA dataset, one needs to check the overlap of the annotated gene names.

With the gtf2t2g submodule of oggmap and the gtf2t2g.parse_gtf() function, one can extract gene and transcript names from a given gene feature file.

How to match gene or transcript IDs between an orthomap and scRNA data

Please download the notebooks from here or please click below to view the content.

• oggmap: Step 3 - map gene/transcript IDs
  • Notebook file
  • Import libraries
  • Import oggmap python package submodules
  • Step 0, Step 1 and Step 2
    • Step 0 - run OrthoFinder
    • Step 1 - get taxonomic information
    • Step 2 - gene age class assignment
  • Step 3 - map OrthoFinder gene names and scRNA gene/transcript names
    • Import now, the scRNA dataset of the query species
    • Get an overview of observations
    • Helper functions to match gene names
    • Reduce isoforms to genes